cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6720095.v2
title: The Latent Scale Covariogram: A Tool for Exploring the Spatial Dependence Structure of Nonnormal Responses

description: When modeling spatially distributed normal responses <i>Y<sub>i</sub></i> in terms of vectors <b>x</b><sub><i>i</i></sub> of explanatory variables, one may fit a linear model assuming independence, and then use the empirical variogram of the residuals to determine an appropriate parametric form for the autocorrelation function. Suppose, however, that the responses are not normally distributed—for example, Poisson or Bernoulli. One may model spatial dependence using a hierarchical generalized linear model in which, conditional on a latent Gaussian field <b>Z</b> = {<i>Z<sub>i</sub></i>}, the <i>Y<sub>i</sub></i> have independent distributions from the exponential family, with an appropriate link function connecting their conditional means with the linear predictors <b>x</b><sup><i>t</i></sup><sub><i>i</i></sub><b>β</b> + <i>Z<sub>i</sub></i>. The question then is how to determine an appropriate model for the autocorrelation function of <b>Z</b>. The empirical variogram of the <i>Y<sub>i</sub></i> is no longer appropriate, since (unless the link function is the identity) it is on the wrong scale. We propose here an alternative, the latent scale covariogram, whose graph reflects the autocorrelation structure of the underlying normal field. We illustrate its use on several real datasets, together with a simulated dataset, and obtain results quite different from those obtained using the variogram. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6720095.v1
title: The Latent Scale Covariogram: a Tool for Exploring the Spatial Dependence Structure of Non-normal Responses

description: When modeling spatially distributed normal responses <i>Y</i><sub><i>i</i></sub> in terms of vectors <b>x</b><sub><i>i</i></sub> of explanatory variables, one may fit a linear model assuming independence, and then use the empirical variogram of the residuals to determine an appropriate parametric form for the autocorrelation function. Suppose, however, that the responses are not normally distributed - for example, Poisson or Bernoulli. One may model spatial dependence using a hierarchical generalized linear model in which, conditional on a latent Gaussian field <b>Z</b> = {<i>Z</i><sub><i>i</i></sub>}, the <i>Y</i><sub><i>i</i></sub> have independent distributions from the exponential family, with an appropriate link function connecting their conditional means with the linear predictors <b>x</b><sup><i>t</i></sup><sub><i>i</i></sub><b>β</b> + <i>Z<sub>i</sub></i>. The question then is how to determine an appropriate model for the autorcorrelation function of <b>Z</b>. The empirical variogram of the <i>Y</i><sub><i>i</i></sub> is no longer appropriate, since (unless the link function is the identity) it is on the wrong scale. We propose here an alternative, the latent scale covariogram, whose graph reflects the autocorrelation structure of the underlying normal field. We illustrate its use on several real data sets, together with a simulated data set, and obtain results quite different from those obtained using the variogram.
DOI: 10.6084/m9.figshare.6719963
title: Occupancy data

description: Burrow occupancy was estimated using ground-based methods. We used 25 quadrants of 20 m x 20 m randomly selected. Each corner was marked with wooden stakes and locations recorded with GPS. We separated the quadrats in three categories ,based on burrow density. Burrows were monitored in April, May, and June 2016, and June 2017, and occupancy was estimated using toothpicks placed at the entrance of the burrows. We monitored 1,342 burrows with toothpicks.
DOI: 10.6084/m9.figshare.6719963.v1
title: Occupancy data

description: Burrow occupancy was estimated using ground-based methods. We used 25 quadrants of 20 m x 20 m randomly selected. Each corner was marked with wooden stakes and locations recorded with GPS. We separated the quadrats in three categories ,based on burrow density. Burrows were monitored in April, May, and June 2016, and June 2017, and occupancy was estimated using toothpicks placed at the entrance of the burrows. We monitored 1,342 burrows with toothpicks.
DOI: 10.6084/m9.figshare.6719906
title: A new cut-based genetic algorithm for graph partitioning applied to cell formation: Supplementary material

description: This document contains additional information (the examples' data tables) to the paper entitled "A new cut-based genetic algorithm for graph partitioning applied to cell formation"accepted in the META18 conference (7<sup>th</sup> International Conference on Metaheuristics and Nature Inspired Computing, Morroco)<br>
DOI: 10.6084/m9.figshare.6719906.v1
title: A new cut-based genetic algorithm for graph partitioning applied to cell formation: Supplementary material

description: This document contains additional information (the examples' data tables) to the paper entitled "A new cut-based genetic algorithm for graph partitioning applied to cell formation"accepted in the META18 conference (7<sup>th</sup> International Conference on Metaheuristics and Nature Inspired Computing, Morroco)<br>
DOI: 10.6084/m9.figshare.6716534
title: Potential of near-infrared fluorescence image-guided debridement in trauma surgery

description: This case report presents the use of near-infrared fluorescence (NIRF) imaging using indocyanine green (ICG) and its potential for the evaluation of soft tissue viability in a traumatic case. Standard implementation of this novel imaging modality might decrease the number of surgical debridement procedures in complex traumatic wounds.
DOI: 10.6084/m9.figshare.6716534.v2
title: Potential of near-infrared fluorescence image-guided debridement in trauma surgery

description: This case report presents the use of near-infrared fluorescence (NIRF) imaging using indocyanine green (ICG) and its potential for the evaluation of soft tissue viability in a traumatic case. Standard implementation of this novel imaging modality might decrease the number of surgical debridement procedures in complex traumatic wounds.
DOI: 10.6084/m9.figshare.6716534.v1
title: Potential of near-infrared fluorescence image-guided debridement in trauma surgery

description: This case report presents the use of near-infrared fluorescence (NIRF) imaging using indocyanine green (ICG) and its potential for the evaluation of soft tissue viability in a traumatic case. Standard implementation of this novel imaging modality might decrease the number of surgical debridement procedures in complex traumatic wounds.
DOI: 10.6084/m9.figshare.12890672
title: Plateosaurus skulls Frick

description: Photogrammetric models of skull material of Plateosaurus from Frick, Switzerland. Dataset contains a total of 12 models in .ply format.<br>Supplementary information for Lallensack et al., submitted<br><br>
DOI: 10.6084/m9.figshare.6716426
title: Figure 4: Crystallization of lunar magma ocean

description: The data of lunar magma ocean crystallization modeled by the software alphaMELTS. The attached .txt file corresponds to Figure 4.<br>The information of bulk composition derives from O'Neil (1990). For trace element see Taylor (1992).<br>In the data file, the first column represents radius (in km), the second column represents temperature (in K), the third column represents density (in kg m^-3) and the fourth column represents initial heat production rate (in W kg-1).
DOI: 10.6084/m9.figshare.6716426.v2
title: Figure 4: Crystallization of lunar magma ocean

description: The data of lunar magma ocean crystallization modeled by the software alphaMELTS. The attached .txt file corresponds to Figure 4.<br>The information of bulk composition derives from O'Neil (1990). For trace element see Taylor (1992).<br>In the data file, the first column represents radius (in km), the second column represents density, the third column represents temperature and the fourth column represents initial heat production rate.
DOI: 10.6084/m9.figshare.6716426.v1
title: Crystallization of lunar magma ocean

description: The data of lunar magma ocean crystallization modeled by the software alphaMELTS.
DOI: 10.6084/m9.figshare.6716333
title: Dengue Virus Primers and Probes from Parental and offspring larval diets interact to influence life-history traits and infection with dengue virus in <i>Aedes aegypti</i>

description: Dengue-1 serotype specific primers and probes designed by Callahan et al. 2001.
DOI: 10.6084/m9.figshare.6716333.v1
title: Dengue Virus Primers and Probes from Parental and offspring larval diets interact to influence life-history traits and infection with dengue virus in <i>Aedes aegypti</i>

description: Dengue-1 serotype specific primers and probes designed by Callahan et al. 2001.
DOI: 10.6084/m9.figshare.12890849.v1
title: Sample Information

description: Excel spreadsheet with sample information.
DOI: 10.6084/m9.figshare.12890849
title: Sample Information

description: Excel spreadsheet with sample information.
DOI: 10.6084/m9.figshare.6716015
title: Herramientas de Educación Nutritional. Cotopaxi

description: Estas son herramientas diseñadas para la educación de niños en Cotopaxi. El diseño pertenece a ESPOL - FCV - EDCOM.<br>
DOI: 10.6084/m9.figshare.6716015.v1
title: Herramientas de Educación Nutritional. Cotopaxi

description: Estas son herramientas diseñadas para la educación de niños en Cotopaxi. El diseño pertenece a ESPOL - FCV - EDCOM.<br>
DOI: 10.6084/m9.figshare.6715988
title: Qualitative and Quantitative Data

description: The information in this data set are raw one on one interviews. Additionally, quantitative data output is included.
DOI: 10.6084/m9.figshare.6715940
title: Compilation of process-based embodied flows for Chilean building materials

description: Compilation of publicly available environmental flows for Chilean building materials extracted from various sources. Work in progress, more data and details to be published.
DOI: 10.6084/m9.figshare.6715940.v1
title: Compilation of embodied flows for Chilean building materials

description: Compilation of publicly available embodied environmental flows (energy, CO2 and water) for Chilean building materials extracted from environmental product declarations (EPDs) and research projects. Work in progress, more details to be published.
DOI: 10.6084/m9.figshare.6715940.v2
title: Compilation of process-based embodied flows for Chilean building materials

description: Compilation of publicly available environmental flows for Chilean building materials extracted from various sources. Work in progress, more data and details to be published.
DOI: 10.6084/m9.figshare.6715940.v3
title: Compilation of process-based embodied flows for Chilean building materials

description: Compilation of publicly available environmental flows for Chilean building materials extracted from various sources. Work in progress, more data and details to be published.
DOI: 10.6084/m9.figshare.6715754
title: Data MixoBioGeo Faure et al. 2018

description: <b>TabV9</b>: Sequence abundance for the 318054 metabarcodes assigned to mixotrophic species sampled during the <i>Tara Oceans</i> campaign.<br><br><b>TabMixo</b>: Sequence abundance table for 133 mixotrophic lineages sampled during the <i>Tara Oceans</i> metabarcoding dataset.<br><br><b>Envi_context</b>: Environmental context data for the studied samples.<br><br><b>Mixotype</b>: Vector of mixotypes for the 133 mixotrophic lineages considered in the study.<br><br><b>V92Mixotype</b>: Vector of mixotypes for the 318054 mixotrophic metabarcodes considered in the study.<br><b>Figure 1 & Figure 4</b>: Coloured versions of figure 1 and 4 appearing in black and white on the online PDF.<br><br>
DOI: 10.6084/m9.figshare.6715718
title: 16S rRNA custom database 01/18

description: 16S rRNA custom database derived from RDP (release 11, update 5) containing only high quality, classified sequences from bacterial isolates. Titles of the sequences are renamed according to taxonomy of each isolate. <br>After building a database by makeblastdb command, this can be used for BLASTing community data.Database created 01/18.<br>
DOI: 10.6084/m9.figshare.6715718.v1
title: 16S rRNA custom database 01/18

description: 16S rRNA custom database derived from RDP (release 11, update 5) containing only high quality, classified sequences from bacterial isolates. Titles of the sequences are renamed according to taxonomy of each isolate. <br>After building a database by makeblastdb command, this can be used for BLASTing community data.Database created 01/18.<br>
DOI: 10.6084/m9.figshare.6715571
title: Lysosomes

description: Movies of fluorescently labelled lysosomes acquired in living cells
DOI: 10.6084/m9.figshare.6715568
title: LY Excell

description: iMSD analysis output of lysosomes movies
DOI: 10.6084/m9.figshare.6715562
title: LE Excell

description: iMSD analysis output of late endosomes movies
DOI: 10.6084/m9.figshare.6715562.v1
title: LE Excell

description: iMSD analysis output of late endosomes movies
DOI: 10.6084/m9.figshare.6715556
title: Late Endosomes

description: Movies of fluorescently labelled late endosomes acquired in living cells
DOI: 10.6084/m9.figshare.6715553
title: EE Excell

description: iMSD analysis output on early endosomes movie
DOI: 10.6084/m9.figshare.6715553.v1
title: EE Excell

description: iMSD analysis output on early endosomes movie
DOI: 10.6084/m9.figshare.6715550
title: Early Endosome

description: Movies of fluorescently labelled early endosomes acquired in living cells
DOI: 10.6084/m9.figshare.6715550.v1
title: Early Endosome

description: Movies of fluorescently labelled early endosomes acquired in living cells
DOI: 10.6084/m9.figshare.6715517
title: Supplementary Material for: Temporal and Vertical Variation in Microbial Community Composition in Response to Physicochemical Characteristics in a Water Column of Highly Eutrophied Jinhae Bay, South Korea

description: Microbial communities play an essential role in marine biogeochemical cycles. Physical and biogeochemical changes in Jinhae Bay, the most anthropogenically eutrophied bay on the coasts of South Korea, are well described, but less is known about the associated changes in microbial communities. Temporal and vertical variation in microbial communities at three depths (surface, middle, and bottom) at seven time points (June to December) at the J1 sampling site were investigated on the MiSeq platform based on the 16S rRNA gene. Overall, the microbial community was dominated by Proteobacteria, Cyanobacteria, and Bacteroidetes from June to November, whereas Firmicutes were dominant in December, especially in the middle and bottom layers. The results indicate that the microbial community composition strongly varied with temporal changes in the physicochemical water properties. Moreover, the community composition differed markedly between the surface and middle layers and the bottom layer in the summer, when the water column was strongly stratified and bottom water hypoxia developed. A redundancy analysis suggested a significant correlation between physicochemical variables (i.e., temperature, salinity, and oxygen concentration) and microbial community composition. This study indicates that temporal changes in water conditions and eutrophication-induced hypoxia effectively shape the structure of the microbial community.
DOI: 10.6084/m9.figshare.6715463
title: Supplementary Material for: MRI Changes in the Thalamus and Basal Ganglia of Full-Term Neonates with Perinatal Asphyxia

description: <b><i>Background:</i></b> Magnetic resonance imaging (MRI) is the standard neuroimaging technique to assess perinatal asphyxia-associated brain injury in full-term infants. Diffusion-weighted imaging (DWI) is most informative when assessed during the first week after the insult. <b><i>Objectives:</i></b> To study the DWI abnormalities of the thalamus and basal ganglia in full-term infants with perinatal asphyxia. <b><i>Methods:</i></b> Fifty-five (near) term infants (normothermia <i>n</i> = 23; hypothermia <i>n</i> = 32) with thalamus and/or basal ganglia injury were included. MRI findings were assessed visually and quantitatively calculating apparent diffusion coefficient (ADC) values. Thalamus/basal ganglia ADC ratios were calculated to analyze the differences between these areas. Infants with an early MRI (days 1–3) or later MRI (days 4–7) were compared. <b><i>Results:</i></b> Isolated extensive thalamic injury was seen early, and focal thalamic and basal ganglia injury was seen later. On the early MRI, visual assessment underestimated abnormalities in the basal ganglia (59% abnormal vs. 90% abnormal on quantitative assessment; <i>p</i> = 0.015), suggesting the need for quantitative assessment. In infants treated with hypothermia, the thalamus/basal ganglia ADC ratio was lower. <b><i>Conclusions:</i></b> Both visual analysis and quantitative evaluation of cerebral MRI after perinatal asphyxia are needed, especially during the first few days after birth. Timing of ADC changes is influenced by therapeutic hypothermia.
DOI: 10.6084/m9.figshare.6715463.v1
title: Supplementary Material for: MRI Changes in the Thalamus and Basal Ganglia of Full-Term Neonates with Perinatal Asphyxia

description: <b><i>Background:</i></b> Magnetic resonance imaging (MRI) is the standard neuroimaging technique to assess perinatal asphyxia-associated brain injury in full-term infants. Diffusion-weighted imaging (DWI) is most informative when assessed during the first week after the insult. <b><i>Objectives:</i></b> To study the DWI abnormalities of the thalamus and basal ganglia in full-term infants with perinatal asphyxia. <b><i>Methods:</i></b> Fifty-five (near) term infants (normothermia <i>n</i> = 23; hypothermia <i>n</i> = 32) with thalamus and/or basal ganglia injury were included. MRI findings were assessed visually and quantitatively calculating apparent diffusion coefficient (ADC) values. Thalamus/basal ganglia ADC ratios were calculated to analyze the differences between these areas. Infants with an early MRI (days 1–3) or later MRI (days 4–7) were compared. <b><i>Results:</i></b> Isolated extensive thalamic injury was seen early, and focal thalamic and basal ganglia injury was seen later. On the early MRI, visual assessment underestimated abnormalities in the basal ganglia (59% abnormal vs. 90% abnormal on quantitative assessment; <i>p</i> = 0.015), suggesting the need for quantitative assessment. In infants treated with hypothermia, the thalamus/basal ganglia ADC ratio was lower. <b><i>Conclusions:</i></b> Both visual analysis and quantitative evaluation of cerebral MRI after perinatal asphyxia are needed, especially during the first few days after birth. Timing of ADC changes is influenced by therapeutic hypothermia.
DOI: 10.6084/m9.figshare.6715349
title: Datasets for follicular cells and C-cells deconvolved by cell frequency from microarray expression data of thyroid tissue from mice i.v. injected with 90 kBq iodine-131 or mock-treated (24-hour time point).xlsx

description: Transcript expression data [GSE66303] from mouse thyroid that received 5.9 Gy from i.v. administered 90 kBq iodine-131 over 24 h (or 0 Gy from physiological saline as control) were deconvolved by cell frequency (cF) for follicular cells (cF=0.89) and C-cells (cF=0.11) using csSAM package version 1.2.4 and R version 3.0.1. The data consists of four sets, i.e. one treated group and one control group for (deconvolved) follicular cells and C-cells, with four replicates per group. For further details, please refer to metadata information given in the data file.<br>
DOI: 10.6084/m9.figshare.6715349.v1
title: Datasets for follicular cells and C-cells deconvolved by cell frequency from microarray expression data of thyroid tissue from mice i.v. injected with 90 kBq iodine-131 or mock-treated (24-hour time point).xlsx

description: Transcript expression data [GSE66303] from mouse thyroid that received 5.9 Gy from i.v. administered 90 kBq iodine-131 over 24 h (or 0 Gy from physiological saline as control) were deconvolved by cell frequency (cF) for follicular cells (cF=0.89) and C-cells (cF=0.11) using csSAM package version 1.2.4 and R version 3.0.1. The data consists of four sets, i.e. one treated group and one control group for (deconvolved) follicular cells and C-cells, with four replicates per group. For further details, please refer to metadata information given in the data file.<br>
DOI: 10.6084/m9.figshare.6715331
title: Antigenotoxic potential of boron nitride nanotubes

description: Boron and boron nitride nanotubes (BNNTs) are increasingly used in different industrial fields and, potentially, in some biomedical areas. As occurs with other nanomaterials (NMs), to increase our knowledge on their potential health hazards is a priority. Although <i>in vitro</i> approaches are a routine in getting biological information on the biological effects of NMs, the use of simple <i>in vivo</i> model organisms is receiving an increased interest. In this context, <i>Drosophila melanogaster</i> is widely used as a eukaryotic model for the study of the potential harmful effects associated with various agents, including NMs. The aim of this study is to provide new data on the potential antioxidant/antigenotoxic properties of boron and boron nitride nanotubes (BNNTs), as well as on other biological end-points. Our results show changes in the expression of genes involved in the antioxidant defense (<i>CAT</i> and <i>SOD</i>), and in those rel0061ted to the integrity of the intestinal barrier (<i>Duox</i>, <i>Hml</i>, <i>Muc68D</i>, and <i>PPO2</i>), at the highest exposure doses (5, 10 mM). However, non-relevant toxic or genotoxic effects were observed. Interestingly, BNNTs and boron significantly reduced the genotoxic effect of potassium dichromate (PDC), and the intracellular levels of reactive oxygen species (ROS). This suggest that the observed effects can be linked to the antioxidant properties of BNNTs and boron. This is the first study reporting antigenotoxicity/genotoxicity, and gene expression data, in the somatic cells of <i>D. melanogaster</i> larvae for BNNTs.
DOI: 10.6084/m9.figshare.6715331.v1
title: Antigenotoxic potential of boron nitride nanotubes

description: Boron and boron nitride nanotubes (BNNTs) are increasingly used in different industrial fields and, potentially, in some biomedical areas. As occurs with other nanomaterials (NMs), to increase our knowledge on their potential health hazards is a priority. Although <i>in vitro</i> approaches are a routine in getting biological information on the biological effects of NMs, the use of simple <i>in vivo</i> model organisms is receiving an increased interest. In this context, <i>Drosophila melanogaster</i> is widely used as a eukaryotic model for the study of the potential harmful effects associated with various agents, including NMs. The aim of this study is to provide new data on the potential antioxidant/antigenotoxic properties of boron and boron nitride nanotubes (BNNTs), as well as on other biological end-points. Our results show changes in the expression of genes involved in the antioxidant defense (<i>CAT</i> and <i>SOD</i>), and in those rel0061ted to the integrity of the intestinal barrier (<i>Duox</i>, <i>Hml</i>, <i>Muc68D</i>, and <i>PPO2</i>), at the highest exposure doses (5, 10 mM). However, non-relevant toxic or genotoxic effects were observed. Interestingly, BNNTs and boron significantly reduced the genotoxic effect of potassium dichromate (PDC), and the intracellular levels of reactive oxygen species (ROS). This suggest that the observed effects can be linked to the antioxidant properties of BNNTs and boron. This is the first study reporting antigenotoxicity/genotoxicity, and gene expression data, in the somatic cells of <i>D. melanogaster</i> larvae for BNNTs.