cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9249023
title: Quantification Figure 3 (GraphPad Prism file)

description: Cytokines and BDNF secretion from human iPSC-derived astrocytes. Conditioned media were collected after stimulating cells during 24 h with 10 ng/mL TNF-α. Cytokines and BDNF secretion was measured in the conditioned media and compared with cells treated with vehicle. (a) - Pro-inflammatory cytokines: Interleukin-1 beta (IL-1β), Interleukin-8 (IL-8), Interferon gamma (IFN-γ) and Tumor necrosis factor alpha (TNF-α); (b) - modulatory cytokines: Interleukin-2 (IL-2), Interleukin-4 (IL-4) and Interleukin-6 (IL-6); (c) - anti-inflammatory cytokines Interleukin-10 (IL-10), Interleukin-13 (IL-13) and Brain-derived neurotrophic factor (BDNF). Data are presented as means ± SEM of concentrations in (pg/ml) of secreted factors. Conditioned media were collected from 4 cell lines and the experiments were performed in duplicates. *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; ns - non-significant. Unpaired Student´s t-test.
DOI: 10.6084/m9.figshare.9249020
title: Quantification Figure 6 (GraphPad Prism file)

description: Impairment of [3H] D-aspartate uptake by TNF-α in human iPSC-derived astrocytes.Aspartate uptake was carried out (a) – 1 day or (b) – 5 days after exposing cells to vehicle or 10 ng/mL TNF-α. The competitive inhibitor of glutamate transporters DL-TBOA was added 10 minutes prior to aspartate. Data are presented as means ± SEM of the percentage of counts per minute (cpm). (c) – Cell viability was evaluated by ethidium incorporation. As a positive control for cell death, cells were lysed with Triton 2 %. As a positive control for cell viability, cells grown in DMEM/F12 with 10 % SFB were also evaluated. Data are presented as means ± SEM of the percentage of ethidium incorporation (arbitrary units of fluorescence). Data from 3 cell lines and experiments were performed in duplicates (a), (b) and quadruplicates (c). *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; One-way ANOVA followed by Tukey post hoc test. ns – Non-significant.
DOI: 10.6084/m9.figshare.9249026.v1
title: Figure 4

description: (a) – Interleukin-6; (b) – Interleukin-1 beta and (c) – TNF-α expression was assessed 24 h after exposing cells to vehicle or 10 ng/mL TNF-α. Data are presented as means ± SEM of fold change for (a) and (b) and Ct (c) since the basal levels of TNF-α were below the limit of quantification in non-stimulated cells. Experiments were performed in triplicates from 4 cell lines. *P &lt; 0.05; N.D. non detected. Unpaired Student´s t-test.
DOI: 10.6084/m9.figshare.9249020.v1
title: Figure 6

description: Impairment of [3H] D-aspartate uptake by TNF-α in human iPSC-derived astrocytes.Aspartate uptake was carried out (a) – 1 day or (b) – 5 days after exposing cells to vehicle or 10 ng/mL TNF-α. The competitive inhibitor of glutamate transporters DL-TBOA was added 10 minutes prior to aspartate. Data are presented as means ± SEM of the percentage of counts per minute (cpm). (c) – Cell viability was evaluated by ethidium incorporation. As a positive control for cell death, cells were lysed with Triton 2 %. As a positive control for cell viability, cells grown in DMEM/F12 with 10 % SFB were also evaluated. Data are presented as means ± SEM of the percentage of ethidium incorporation (arbitrary units of fluorescence). Data from 3 cell lines and experiments were performed in duplicates (a), (b) and quadruplicates (c). *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; One-way ANOVA followed by Tukey post hoc test. ns – Non-significant.
DOI: 10.6084/m9.figshare.9249023.v1
title: Figure 3

description: Cytokines and BDNF secretion from human iPSC-derived astrocytes. Conditioned media were collected after stimulating cells during 24 h with 10 ng/mL TNF-α. Cytokines and BDNF secretion was measured in the conditioned media and compared with cells treated with vehicle. (a) - Pro-inflammatory cytokines: Interleukin-1 beta (IL-1β), Interleukin-8 (IL-8), Interferon gamma (IFN-γ) and Tumor necrosis factor alpha (TNF-α); (b) - modulatory cytokines: Interleukin-2 (IL-2), Interleukin-4 (IL-4) and Interleukin-6 (IL-6); (c) - anti-inflammatory cytokines Interleukin-10 (IL-10), Interleukin-13 (IL-13) and Brain-derived neurotrophic factor (BDNF). Data are presented as means ± SEM of concentrations in (pg/ml) of secreted factors. Conditioned media were collected from 4 cell lines and the experiments were performed in duplicates. *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; ns - non-significant. Unpaired Student´s t-test.
DOI: 10.6084/m9.figshare.9248999
title: Impact of nitrite exposure on related physiological parameters, oxidative stress, and apoptosis in Takifugu rubripes

description: Raw data for plotting
DOI: 10.6084/m9.figshare.9248999.v1
title: Impact of nitrite exposure on related physiological parameters, oxidative stress, and apoptosis in Takifugu rubripes

description: Raw data for plotting
DOI: 10.6084/m9.figshare.9248981
title: Autism spectrum disorders (ASDs) Psynaptic Genes Targeted Sequencing

description: Autism spectrum disorders (ASDs) are characterized by deficits in three core behavioral domains: reciprocal social interactions, communication, and restricted interests and/or repetitive behaviors. It remains a challenge to associate these genes with specific core behavioral deficits. In multiplex autism families, affected sibs often show significant differences in severity of individual core phenotypes. We hypothesize that a higher mutation burden contributes to a larger difference in the severity of specific core phenotypes between affected sibs. We tested this hypothesis on social behavioral deficits in autism. We sequenced synaptome genes (n=1,886) in affected male sib-pairs (n=274) in families from the Autism Genetics Research Exchange (AGRE) and identified rare (MAF≤1%) and predicted functional variants.
DOI: 10.6084/m9.figshare.9248981.v2
title: Autism spectrum disorders (ASDs) Psynaptic Genes Targeted Sequencing

description: Autism spectrum disorders (ASDs) are characterized by deficits in three core behavioral domains: reciprocal social interactions, communication, and restricted interests and/or repetitive behaviors. It remains a challenge to associate these genes with specific core behavioral deficits. In multiplex autism families, affected sibs often show significant differences in severity of individual core phenotypes. We hypothesize that a higher mutation burden contributes to a larger difference in the severity of specific core phenotypes between affected sibs. We tested this hypothesis on social behavioral deficits in autism. We sequenced synaptome genes (n=1,886) in affected male sib-pairs (n=274) in families from the Autism Genetics Research Exchange (AGRE) and identified rare (MAF≤1%) and predicted functional variants.
DOI: 10.6084/m9.figshare.9248903
title: source data for Zhu et al. ms submitted to NC

description: source data for Zhu et al. ms submitted to NC
DOI: 10.6084/m9.figshare.9248981.v1
title: Autism spectrum disorders (ASDs) Targeted (Psynaptic Genes) Sequencing

description: Autism spectrum disorders (ASDs) are characterized by deficits in three core behavioral domains: reciprocal social interactions, communication, and restricted interests and/or repetitive behaviors. It remains a challenge to associate these genes with specific core behavioral deficits. In multiplex autism families, affected sibs often show significant differences in severity of individual core phenotypes. We hypothesize that a higher mutation burden contributes to a larger difference in the severity of specific core phenotypes between affected sibs. We tested this hypothesis on social behavioral deficits in autism. We sequenced synaptome genes (n=1,886) in affected male sib-pairs (n=274) in families from the Autism Genetics Research Exchange (AGRE) and identified rare (MAF≤1%) and predicted functional variants.
DOI: 10.6084/m9.figshare.9248897
title: Intraoperative computed tomography imaging for dose calculation in intraoperative electron radiation therapy: data, code and tables

description: This dataset (DataSet_Code.zip) contains all exposure data, and the 3D dose distributions, 3D masks and code used in the 3D Gamma analyses of the article “Intraoperative computed tomography imaging for dose calculation in intraoperative electron radiation therapy: Initial clinical observations” by Verónica García-Vázquez, Felipe A. Calvo, María J. Ledesma-Carbayo, Claudio V. Sole, José Calvo-Haro, Manuel Desco and Javier Pascau. We have also uploaded the tables of this article (Tables.pdf) to this Figshare repository without the wrong extra lines added by the journal PLOS ONE in its published version: https://doi.org/10.1371/journal.pone.0227155.<br>Overview of DataSet_Code.zip: • The folder “Exposure” contains the exposure data of every acquired computed tomography (CT) study. Data saved as XLSX files. • The folder “Patient1” contains the five 3D dose distributions calculated from the Patient 1’s preoperative and intraoperative data, and the 3D mask used in the Gamma analyses. Patient 1’s diagnosis: Ewing sarcoma. 3D images in Analyze format. • The folder “Patient2” contains the five 3D dose distributions calculated from the Patient 2’s preoperative and intraoperative data, and the 3D mask used in the Gamma analyses. Patient 2’s diagnosis: Rhabdomyosarcoma. 3D images in Analyze format. • The folder “Patient6” contains the five 3D dose distributions calculated from the Patient 6’s preoperative and intraoperative data, and the 3D mask used in the Gamma analyses. Patient 6’s diagnosis: Chondrosarcoma. 3D images in Analyze format. • The file “gammaAnalyses.py” is the Python code used to calculate the percentage of voxels fulfilling the 3D Gamma criteria when comparing dose distributions. • The file “ReadMe.txt” contains this description.
DOI: 10.6084/m9.figshare.9248903.v1
title: source data for Zhu et al. ms submitted to NC

description: source data for Zhu et al. ms submitted to NC
DOI: 10.6084/m9.figshare.9248897.v1
title: Intraoperative computed tomography imaging for dose calculation in intraoperative electron radiation therapy: data and code

description: This dataset contains all exposure data, and the 3D dose distributions, 3D masks and code used in the 3D Gamma analyses of the article “Intraoperative computed tomography imaging for dose calculation in intraoperative electron radiation therapy: initial clinical observations” by Verónica García-Vázquez, Felipe A. Calvo, María J. Ledesma-Carbayo, Claudio V. Sole, José Calvo-Haro, Manuel Desco and Javier Pascau.<br>Overview: • The folder “Exposure” contains the exposure data of every acquired computed tomography (CT) study. Data saved as XLSX files. • The folder “Patient1” contains the five 3D dose distributions calculated from the Patient 1’s preoperative and intraoperative data, and the 3D mask used in the Gamma analyses. Patient 1’s diagnosis: Ewing sarcoma. 3D images in Analyze format. • The folder “Patient2” contains the five 3D dose distributions calculated from the Patient 2’s preoperative and intraoperative data, and the 3D mask used in the Gamma analyses. Patient 2’s diagnosis: Rhabdomyosarcoma. 3D images in Analyze format. • The folder “Patient6” contains the five 3D dose distributions calculated from the Patient 6’s preoperative and intraoperative data, and the 3D mask used in the Gamma analyses. Patient 6’s diagnosis: Chondrosarcoma. 3D images in Analyze format. • The file “gammaAnalyses.py” is the Python code used to calculate the percentage of voxels fulfilling the 3D Gamma criteria when comparing dose distributions. • The file “ReadMe.txt” contains this description.
DOI: 10.6084/m9.figshare.9248903.v2
title: source data for Zhu et al. ms submitted to NC

description: source data for Zhu et al. ms submitted to NC
DOI: 10.6084/m9.figshare.9248903.v4
title: source data for Zhu et al. ms submitted to NC

description: source data for Zhu et al. ms submitted to NC
DOI: 10.6084/m9.figshare.9248864
title: The human gut virome is highly diverse, stable and individual-specific.

description: The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterised and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of faecal viruses in healthy adults which reveal high temporal stability, individual specificity and correlation with the bacterial microbiome. Using a database independent approach which uses most of the sequencing data we report the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and <i>Microviridae</i> bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as <i>Bacteroides</i>, <i>Prevotella</i> and <i>Faecalibacterium</i>. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.
DOI: 10.6084/m9.figshare.9248903.v3
title: source data for Zhu et al. ms submitted to NC

description: source data for Zhu et al. ms submitted to NC
DOI: 10.6084/m9.figshare.9248849
title: Validation of a scale to evaluate acute pain in donkeys (Equus asinus)

description: O objetivo deste estudo foi avaliar a validade de uma escala para avaliar a dor aguda em burros.
DOI: 10.6084/m9.figshare.9248822
title: Dataset of dissolved oxygen and carbonate parameters supporting the study entitled as "Emergence of summertime hypoxia and concurrent carbonate mineral suppression in the central Bohai Sea, China"

description: Between August 2011 and September 2017, eight field surveys were conducted in the central Bohai Sea, spanning all four seasons. To examine possible intra-seasonal and inter-annual variations in summertime DO depletion and concurrent carbonate mineral suppression, one July data set and two August data sets and two September data sets were investigated in this study, although these summer and/or early autumn surveys distributed over different years. During these surveys, water samples were collected at 9–37 grid stations for the measurements of DO, pH, total alkalinity (TAlk), and dissolved inorganic carbon (DIC). Most sampling stations had a water depth of 15–35 m.
DOI: 10.6084/m9.figshare.9248849.v1
title: Validation of a scale to evaluate acute pain in donkeys (Equus asinus)

description: O objetivo deste estudo foi avaliar a validade de uma escala para avaliar a dor aguda em burros.
DOI: 10.6084/m9.figshare.9248795
title: Impact of nitrite exposure on plasma biochemical parameters and immune related response in Takifugu rubripes

description: Data Availability Statement
DOI: 10.6084/m9.figshare.9248786
title: RVOT&LVOT Diagnosis

description: The 12-lead ECG data analysis is a reliable tool to ascertain the locations of premature ventricular contractions or ventricular tachycardia and determine the locations of subsequent catheter ablation procedure. The majority of idiopathic ventricular arrhythmia, outflow tract ventricular arrhythmia stem from either the right ventricular outflow tract or the left ventricular outflow tract. We created a new 12-lead ECG database that was created under the auspices of Chapman University and Ningbo First Hospital of Zhejiang University with the intention to provide high quality evidence revealing the distinction between idiopathic ventricular arrhythmia from right ventricular outflow tract to left ventricular outflow tract. The dataset contains 334 subjects who not only experienced idiopathic premature ventricular contractions or ventricular tachycardia but also had successfully undergone a catheter ablation procedure that validated the accurate origins of idiopathic ventricular arrhythmia.
DOI: 10.6084/m9.figshare.9248822.v1
title: Dataset of dissolved oxygen and carbonate parameters supporting the study entitiled as "Emergence of summertime hypoxia and concurrent carbonate mineral suppression in the central Bohai Sea, China"

description: Between August 2011 and September 2017, eight field surveys were conducted in the central Bohai Sea, spanning all four seasons. To examine possible intra-seasonal and inter-annual variations in summertime DO depletion and concurrent carbonate mineral suppression, one July data set and two August data sets and two September data sets were investigated in this study, although these summer and/or early autumn surveys distributed over different years. During these surveys, water samples were collected at 9–37 grid stations for the measurements of DO, pH, total alkalinity (TAlk), and dissolved inorganic carbon (DIC). Most sampling stations had a water depth of 15–35 m.
DOI: 10.6084/m9.figshare.9248795.v3
title: Impact of nitrite exposure on plasma biochemical parameters and immune related response in Takifugu rubripes

description: Data Availability Statement
DOI: 10.6084/m9.figshare.9248822.v2
title: Dataset of dissolved oxygen and carbonate parameters supporting the study entitled "Emergence of summertime hypoxia and concurrent carbonate mineral suppression in the central Bohai Sea, China"

description: Between August 2011 and September 2017, eight field surveys were conducted in the central Bohai Sea, spanning all four seasons. To examine possible intra-seasonal and inter-annual variations in summertime DO depletion and concurrent carbonate mineral suppression, one July data set and two August data sets and two September data sets were investigated in this study, although these summer and/or early autumn surveys distributed over different years. During these surveys, water samples were collected at 9–37 grid stations for the measurements of DO, pH, total alkalinity (TAlk), and dissolved inorganic carbon (DIC). Most sampling stations had a water depth of 15–35 m.
DOI: 10.6084/m9.figshare.9248483
title: Raw data of AFLP for Paris polyphylla var. yunnanensis.xlsx

description: Paris polyphylla var. yunnanensis is an important medicinal plant. In this study, AFLP markers were adopted to reveal genetic diversity and structure of 15 wild and 17 cultivated populations of this species. The "Raw data of AFLP for Paris polyphylla var. yunnanensis.xlsx" file is the raw data of AFLP in this study. Important figures and data were shown in the article published in Ecology and Evolution, named "A comparative study of the population genetics of wild and cultivated populations of Paris polyphylla var. yunnanensis based on AFLP markers".
DOI: 10.6084/m9.figshare.9248483.v1
title: Raw data of AFLP for Paris polyphylla var. yunnanensis.xlsx

description: Paris polyphylla var. yunnanensis is an important medicinal plant. In this study, AFLP markers were adopted to reveal genetic diversity and structure of 15 wild and 17 cultivated populations of this species. The "Raw data of AFLP for Paris polyphylla var. yunnanensis.xlsx" file is the raw data of AFLP in this study. Important figures and data were shown in the article published in Ecology and Evolution, named "A comparative study of the population genetics of wild and cultivated populations of Paris polyphylla var. yunnanensis based on AFLP markers".
DOI: 10.6084/m9.figshare.9247856
title: EnvironmentalCrimes_Categorization.xlsx

description: <pre>These data are categorizations carried out by a researcher of environmental crimes assessed by Brazilian regulatory agencies (ICMBIO and IBAMA) for the purpose of completing a master's degree on deforestation in the region of influence of BR163, which is part of the Legal Amazon.</pre>
DOI: 10.6084/m9.figshare.9247856.v1
title: EnvironmentalCrimes_Categorization.xlsx

description: <pre>These data are categorizations carried out by a researcher of environmental crimes assessed by Brazilian regulatory agencies (ICMBIO and IBAMA) for the purpose of completing a master's degree on deforestation in the region of influence of BR163, which is part of the Legal Amazon.</pre>
DOI: 10.6084/m9.figshare.9247838
title: Soil Moisture and Vegetation Optical Depth SMAP Retrievals in Insular Southeast Asia

description: This repository contains soil moisture and vegetation optical depth (VOD) retrievals from the Multi-Temporal Dual Channel Algorithm applied to SMAP observations. The data are subset for Insular Southeast Asia (ISEA), which encompasses Sumatra, Borneo, and Peninsular Malaysia, as well as the two year period from April 1, 2015 to March 31, 2017.
DOI: 10.6084/m9.figshare.9247838.v1
title: Soil Moisture and Vegetation Optical Depth SMAP Retrievals in Insular Southeast Asia

description: This repository contains soil moisture and vegetation optical depth (VOD) retrievals from the Multi-Temporal Dual Channel Algorithm applied to SMAP observations. The data are subset for Insular Southeast Asia (ISEA), which encompasses Sumatra, Borneo, and Peninsular Malaysia, as well as the two year period from April 1, 2015 to March 31, 2017.
DOI: 10.6084/m9.figshare.9247802
title: PFL-STRUCTURE-2

description: PFL-STRUCTURE-2<br>Optimized geometries of intermediates A-D and transition states TS1-3 starting from structure 2 taken from MD trajectory of non-acetylated (PFL•) topology without CoA in the active site.
DOI: 10.6084/m9.figshare.9247802.v1
title: PFL-STRUCTURE-2

description: PFL-STRUCTURE-2<br>Optimized geometries of intermediates A-D and transition states TS1-3 starting from structure 2 taken from MD trajectory of non-acetylated (PFL•) topology without CoA in the active site.
DOI: 10.6084/m9.figshare.9247670.v1
title: Partial molar properties from molecular simulation using multiple linear regression

description: Partial molar volumes, energies, and enthalpies can be computed from <i>NpT</i>-Gibbs ensemble simulations through a post-processing procedure that leverages fluctuations in composition, total volume, and total energy of a simulation box. By recording the instantaneous box volumes <i>V</i> and instantaneous number of molecules Ni of each of <i>n</i> species for <i>M</i> frames, a large M×n matrix N is constructed, as well as the M×1 vector V. The 1×n vector of partial molar volumes V¯ may then be solved using N⋅V¯=V. A similar construction permits calculation of partial molar energies using <i>M</i> instantaneous measurements of the total energy of the simulation box, and N⋅U¯=U. Partial molar enthalpies may be derived from U¯, V¯, and pressure <i>p</i>. These properties may be used to calculate enthalpy and entropy of transfer (absorption, extraction, and adsorption) for species in complex mixtures. The method is demonstrated on three systems in the <i>NpT</i>-Gibbs ensemble: a highly compressible natural gas condensate of methane, <i>n</i>-butane, and <i>n</i>-decane, the liquid-phase adsorption of 1,5-pentanediol and ethanol onto the MFI zeolite, and a relatively incompressible mixture of ethanol, <i>n</i>-dodecane, and water at liquid-liquid equilibrium. Property predictions are compared to those from numerical differentiation of simulation data sequentially changing the composition and from equations of state. The method can also be extended to reaction equilibria in a closed system and is applied to a reactive first-principles Monte Carlo simulation of compressed nitrogen/oxygen.
DOI: 10.6084/m9.figshare.9247505
title: Additional file 2: of The differential response of cold-experienced Arabidopsis thaliana to larval herbivory benefits an insect generalist, but not a specialist

description: Table S1. List of genes differentially expressed in response to cold treatment and/or feeding by Pieris brassicae larvae, feeding by Mamestra brassicae larvae or artificial wounding. (XLSX 1843 kb)
DOI: 10.6084/m9.figshare.9247505.v1
title: Additional file 2: of The differential response of cold-experienced Arabidopsis thaliana to larval herbivory benefits an insect generalist, but not a specialist

description: Table S1. List of genes differentially expressed in response to cold treatment and/or feeding by Pieris brassicae larvae, feeding by Mamestra brassicae larvae or artificial wounding. (XLSX 1843 kb)