cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3816996.v1
title: Supp Table 4 D398-N398 Functional Analysis.xls

description: <b>Supplemental Table 4. </b>Functional analysis of genes differentially expressed between D398 and N398. Each worksheet is the result of comparing N398 Enriched or D398 Enriched gene lists using DAVID (Huang da, et al., 2009a, b). Abbreviations: GO, gene ontology; BP, biological process; CC, cellular component; MF, molecular function; KEGG, Kyoto encyclopedia of genes and genomes (pathway analysis).
DOI: 10.6084/m9.figshare.3814809
title: ANEXO I. Rubrica Evaluación Etapa Referenciación

description: Rubrica de Evaluación Etapa de Evaluación. Proyecto de Investigación Ambientes Ubicuos en la Investigación Formativa en Educación Superior.
DOI: 10.6084/m9.figshare.3814809.v2
title: ANEXO I. Rubrica Evaluación Etapa Referenciación

description: Rubrica de Evaluación Etapa de Evaluación. Proyecto de Investigación Ambientes Ubicuos en la Investigación Formativa en Educación Superior.
DOI: 10.6084/m9.figshare.3814809.v1
title: ANEXO I. Rubrica Evaluación Etapa Referenciación

description: Rubrica de Evaluación Etapa de Evaluación. Proyecto de Investigación Ambientes Ubicuos en la Investigación Formativa en Educación Superior.
DOI: 10.6084/m9.figshare.3814785
title: Survey_ANOVA.xlsx

description: Survey and experimental datasets for paper "Landscape Position Influences Soil Respiration Variability and Sensitivity to Physiological Drivers in Mixed-use Lands of Southern California, USA." <b> <br></b>
DOI: 10.6084/m9.figshare.3814785.v1
title: Survey_ANOVA.xlsx

description: Survey and experimental datasets for paper "Landscape Position Influences Soil Respiration Variability and Sensitivity to Physiological Drivers in Mixed-use Lands of Southern California, USA." <b> <br></b>
DOI: 10.6084/m9.figshare.3814731
title: Gaussian Job Archive for C44H28N4Pt

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814731.v1
title: Gaussian Job Archive for C44H28N4Pt

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.15131/shef.data.3814701
title: Mechanoregulation of bone remodelling in mice under physiological loading

description: These are the raw data analysed and reported in the manuscript entitled "EVALUATION OF DIFFERENT BONE REMODELLING THEORIES ON THE CHANGES IN BONE MINERAL DENSITY OF MICE TIBIAE UNDER PHYSIOLOGICAL LOADING" by Yongtao Lu, Enrico Dall’Ara, Maya Boudiffa, and Marco Viceconti, submitted for publication to the Journal of the Royal Society Interface. <br>
DOI: 10.15131/shef.data.3814701.v1
title: Mechanoregulation of bone remodelling in mice under physiological loading

description: These are the raw data analysed and reported in the manuscript entitled "EVALUATION OF DIFFERENT BONE REMODELLING THEORIES ON THE CHANGES IN BONE MINERAL DENSITY OF MICE TIBIAE UNDER PHYSIOLOGICAL LOADING" by Yongtao Lu, Enrico Dall’Ara, Maya Boudiffa, and Marco Viceconti, submitted for publication to the Journal of the Royal Society Interface. <br>
DOI: 10.6084/m9.figshare.3814695
title: Gaussian Job Archive for C214H342O18

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814695.v1
title: Gaussian Job Archive for C214H342O18

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814692
title: Gaussian Job Archive for C96H98O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814692.v1
title: Gaussian Job Archive for C96H98O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814689
title: Gaussian Job Archive for C96H98O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814689.v1
title: Gaussian Job Archive for C96H98O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814686
title: Gaussian Job Archive for C96H98O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814686.v1
title: Gaussian Job Archive for C96H98O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814683
title: Gaussian Job Archive for C360H626O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814683.v1
title: Gaussian Job Archive for C360H626O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814680
title: Gaussian Job Archive for C214H342O18

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814680.v1
title: Gaussian Job Archive for C214H342O18

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814674
title: Wilson Disease: Epigenetic effects of choline supplementation on phenotype and clinical course in a mouse model

description: Wilson disease (WD), a genetic disorder affecting copper transport, is characterized by hepatic and neurological manifestations with variable and often unpredictable presentation. Global DNA methylation in liver was previously modified by dietary choline in tx-j mice, a spontaneous mutant model of WD. We therefore hypothesized that the WD phenotype and hepatic gene expression of tx-j offspring could be modified by maternal methyl supplementation during pregnancy. In an initial experiment, female tx-j mice or wild type mice were fed control or choline-supplemented diets 2 weeks prior to mating through embryonic day 17. Transcriptomic analysis (RNA-seq) on embryonic livers revealed tx-j-specific differences in genes related to oxidative phosphorylation, mitochondrial dysfunction, and the neurological disorders Huntington's disease and Alzheimer disease. Maternal choline supplementation restored the transcript levels of a subset of genes to wild type levels. In a separate experiment, a group of tx-j offspring continued to receive choline-supplemented or control diets, with or without the copper chelator penicillamine (PCA) for 12 weeks until 24 weeks of age. Combined choline supplementation and PCA treatment of 24-week-old tx-j mice was associated with increased liver transcript levels of methionine metabolism and oxidative phosphorylation-related genes. Sex differences in gene expression within each treatment group were also observed. These results demonstrate that the transcriptional changes in oxidative phosphorylation and methionine metabolism genes in WD that originate during fetal life are, in part, prevented by prenatal maternal choline supplementation, a finding with potential relevance to preventive treatments of WD.
DOI: 10.6084/m9.figshare.3814674.v2
title: Wilson Disease: Epigenetic effects of choline supplementation on phenotype and clinical course in a mouse model

description: Wilson disease (WD), a genetic disorder affecting copper transport, is characterized by hepatic and neurological manifestations with variable and often unpredictable presentation. Global DNA methylation in liver was previously modified by dietary choline in tx-j mice, a spontaneous mutant model of WD. We therefore hypothesized that the WD phenotype and hepatic gene expression of tx-j offspring could be modified by maternal methyl supplementation during pregnancy. In an initial experiment, female tx-j mice or wild type mice were fed control or choline-supplemented diets 2 weeks prior to mating through embryonic day 17. Transcriptomic analysis (RNA-seq) on embryonic livers revealed tx-j-specific differences in genes related to oxidative phosphorylation, mitochondrial dysfunction, and the neurological disorders Huntington's disease and Alzheimer disease. Maternal choline supplementation restored the transcript levels of a subset of genes to wild type levels. In a separate experiment, a group of tx-j offspring continued to receive choline-supplemented or control diets, with or without the copper chelator penicillamine (PCA) for 12 weeks until 24 weeks of age. Combined choline supplementation and PCA treatment of 24-week-old tx-j mice was associated with increased liver transcript levels of methionine metabolism and oxidative phosphorylation-related genes. Sex differences in gene expression within each treatment group were also observed. These results demonstrate that the transcriptional changes in oxidative phosphorylation and methionine metabolism genes in WD that originate during fetal life are, in part, prevented by prenatal maternal choline supplementation, a finding with potential relevance to preventive treatments of WD.
DOI: 10.6084/m9.figshare.3814674.v1
title: Wilson Disease: epigenetic effects of choline supplementation on phenotype and clinical course in a mouse model

description: Wilson disease (WD), a genetic disorder affecting copper transport, is characterized by hepatic and neurological manifestations with variable and often unpredictable presentation. Global DNA methylation in liver was previously modified by dietary choline in tx-j mice, a spontaneous mutant model of WD. We therefore hypothesized that the WD phenotype and hepatic gene expression of tx-j offspring could be modified by maternal methyl supplementation during pregnancy. In an initial experiment, female tx-j mice or wild type mice were fed control or choline-supplemented diets two weeks prior to mating through embryonic day 17. Transcriptomic analysis (RNA-seq) on embryonic livers revealed tx-j-specific differences in genes related to oxidative phosphorylation, mitochondrial dysfunction, and the neurological disorders Huntington's disease and Alzheimer's disease. Maternal choline supplementation restored the transcript levels of a subset of genes to wild type levels. In a separate experiment, a group of tx-j offspring continued to receive choline-supplemented or control diets, with or without the copper chelator penicillamine (PCA) for 12 weeks until 24 weeks of age. Combined choline supplementation and PCA treatment of 24-week-old tx-j mice was associated with increased liver transcript levels of methionine metabolism and oxidative phosphorylation-related genes. Sex differences in gene expression within each treatment group were also observed. These results demonstrate that the transcriptional changes in oxidative phosphorylation and methionine metabolism genes in WD that originate during fetal life are, in part, prevented by prenatal maternal choline supplementation, a finding with potential relevance to preventive treatments of WD.
DOI: 10.6084/m9.figshare.3814665
title: Data and R code supplement to "What’s scale got to do with it? Models for urban tree canopy"

description: This fileset accompanies this paper:<br>Locke, D. H., Landry, S., Grove, J. M., Roy Chowdhury, R.. (2016). What’s scale got to do with it? Models for urban tree canopy. Journal of Urban Ecology. 2(1): 1-16. DOI: 10.1093/jue/juw006<br><br>The files set contains the single level Census Block Group shapefile (1.3 MB), the two-level *.dbf file (~145 MB), the R script (as an *.rtf) used for the paper, and the resulting zipped *.R file (1.03GB zipped, 1.15GB) created by that script. The two-level polygons are not provided to keep the file size manageable. <br>The script contains the field names and their descriptions, see also Table 1 in the paper.<br>The script will automatically download the data needed to recreate the analyses presented in the paper, but the *.R can be downloaded directly to avoid the running the whole script, which can take up to 12 hours because of the really complex models. <br><br>
DOI: 10.6084/m9.figshare.3814665.v2
title: Data and R code supplement to "What’s scale got to do with it? Models for urban tree canopy"

description: This fileset accompanies this paper:<br>Locke, D. H., Landry, S., Grove, J. M., Roy Chowdhury, R.. (2016). What’s scale got to do with it? Models for urban tree canopy. Journal of Urban Ecology. 2(1): 1-16. DOI: 10.1093/jue/juw006<br><br>The files set contains the single level Census Block Group shapefile (1.3 MB), the two-level *.dbf file (~145 MB), the R script (as an *.rtf) used for the paper, and the resulting zipped *.R file (1.03GB zipped, 1.15GB) created by that script. The two-level polygons are not provided to keep the file size manageable. <br>The script contains the field names and their descriptions, see also Table 1 in the paper.<br>The script will automatically download the data needed to recreate the analyses presented in the paper, but the *.R can be downloaded directly to avoid the running the whole script, which can take up to 12 hours because of the really complex models. <br><br>
DOI: 10.6084/m9.figshare.3814662
title: Familial resemblances in blood leukocyte DNA methylation levels

description: Epigenetic factors such as DNA methylation are DNA alterations affecting gene expression that can convey environmental information through generations. Only a few studies have demonstrated epigenetic inheritance in humans. Our objective is to quantify genetic and common environmental determinants of familial resemblances in DNA methylation levels, using a family based sample. DNA methylation was measured in 48 French Canadians from 16 families as part of the GENERATION Study. We used the Illumina HumanMethylation450 BeadChip array to measure DNA methylation levels in blood leukocytes on 485,577 CpG sites. Heritability was assessed using the variance components method implemented in the QTDT software, which partitions the variance into polygenic (G), common environmental (C), and non-shared environmental (E) effects. We computed maximal heritability, genetic heritability, and common environmental effect for all probes (12.7%, 8.2%, and 4.5%, respectively) and for statistically significant probes (81.8%, 26.9%, and 54.9%, respectively). Higher maximal heritability was observed in the Major Histocompatibility Complex region on chromosome 6. In conclusion, familial resemblances in DNA methylation levels are mainly attributable to genetic factors when considering the average across the genome, but common environmental effect plays an important role when considering statistically significant probes. Further epigenome-wide studies on larger samples combined with genome-wide genotyping studies are needed to better understand the underlying mechanisms of DNA methylation heritability.
DOI: 10.6084/m9.figshare.3814662.v2
title: Familial resemblances in blood leukocyte DNA methylation levels

description: Epigenetic factors such as DNA methylation are DNA alterations affecting gene expression that can convey environmental information through generations. Only a few studies have demonstrated epigenetic inheritance in humans. Our objective is to quantify genetic and common environmental determinants of familial resemblances in DNA methylation levels, using a family based sample. DNA methylation was measured in 48 French Canadians from 16 families as part of the GENERATION Study. We used the Illumina HumanMethylation450 BeadChip array to measure DNA methylation levels in blood leukocytes on 485,577 CpG sites. Heritability was assessed using the variance components method implemented in the QTDT software, which partitions the variance into polygenic (G), common environmental (C), and non-shared environmental (E) effects. We computed maximal heritability, genetic heritability, and common environmental effect for all probes (12.7%, 8.2%, and 4.5%, respectively) and for statistically significant probes (81.8%, 26.9%, and 54.9%, respectively). Higher maximal heritability was observed in the Major Histocompatibility Complex region on chromosome 6. In conclusion, familial resemblances in DNA methylation levels are mainly attributable to genetic factors when considering the average across the genome, but common environmental effect plays an important role when considering statistically significant probes. Further epigenome-wide studies on larger samples combined with genome-wide genotyping studies are needed to better understand the underlying mechanisms of DNA methylation heritability.
DOI: 10.6084/m9.figshare.3814620
title: Improving Factor Score Estimation Through the Use of Observed Background Characteristics

description: A challenge facing nearly all studies in the psychological sciences is how to best combine multiple items into a valid and reliable score to be used in subsequent modeling. The most ubiquitous method is to compute a mean of items, but more contemporary approaches use various forms of latent score estimation. Regardless of approach, outside of large-scale testing applications, scoring models rarely include background characteristics to improve score quality. This article used a Monte Carlo simulation design to study score quality for different psychometric models that did and did not include covariates across levels of sample size, number of items, and degree of measurement invariance. The inclusion of covariates improved score quality for nearly all design factors, and in no case did the covariates degrade score quality relative to not considering the influences at all. Results suggest that the inclusion of observed covariates can improve factor score estimation.
DOI: 10.6084/m9.figshare.3814662.v1
title: Familial Resemblances in Blood Leukocyte DNA Methylation Levels

description: Epigenetic factors such as DNA methylation are DNA alterations affecting gene expression that can convey environmental information through generations. Only a few studies have demonstrated epigenetic inheritance in humans. Our objective is to quantify genetic and common environmental determinants of familial resemblances in DNA methylation levels, using a family based sample. DNA methylation was measured in 48 French Canadians from 16 families as part of the GENERATION Study. We used the Illumina HumanMethylation450 BeadChip array to measure DNA methylation levels in blood leukocytes on 485,577 CpG sites. Heritability was assessed using the variance components method implemented in the QTDT software, which partitions the variance into polygenic (G), common environmental (C), and non-shared environmental (E) effects. We computed maximal heritability, genetic heritability, and common environmental effect for all probes (12.7%, 8.2%, and 4.5%, respectively) and for statistically significant probes (81.8%, 26.9%, and 54.9%, respectively). Higher maximal heritability was observed in the Major Histocompatibility Complex region on chromosome 6. In conclusion, familial resemblances in DNA methylation levels is mainly attributable to genetic factors when considering the average across the genome, but common environmental effect plays an important role when considering statistically significant probes. Further genome-wide studies on larger samples combined with genome-wide association studies are needed to better understand the underlying mechanisms of DNA methylation heritability.
DOI: 10.6084/m9.figshare.3814620.v1
title: Improving Factor Score Estimation Through the Use of Observed Background Characteristics

description: A challenge facing nearly all studies in the psychological sciences is how to best combine multiple items into a valid and reliable score to be used in subsequent modeling. The most ubiquitous method is to compute a mean of items, but more contemporary approaches use various forms of latent score estimation. Regardless of approach, outside of large-scale testing applications, scoring models rarely include background characteristics to improve score quality. This article used a Monte Carlo simulation design to study score quality for different psychometric models that did and did not include covariates across levels of sample size, number of items, and degree of measurement invariance. The inclusion of covariates improved score quality for nearly all design factors, and in no case did the covariates degrade score quality relative to not considering the influences at all. Results suggest that the inclusion of observed covariates can improve factor score estimation.
DOI: 10.6084/m9.figshare.3814602
title: Gaussian Job Archive for C96H98O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814602.v1
title: Gaussian Job Archive for C96H98O24

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.3814599
title: ELE-00371-2016 Si-DIN data set for Ecology Letters.csv

description: Columns in the CSV file are (in order from left to right) lake number in the Iowa state lake surevey, lake name, county, the UTM zone of geographical coordinates of each lake, the easting in meters, the northing in meters, the dissolved silica concentration in micro-molar units (as Si), the dissolved inorganic nitrogen concentration in micro-molar units (as N), the ratio of the two preceding concentrations, the average biomass of diatoms as a percentage of total phytoplankton, the lake area as a percentage of the total watershed area, and agricultural land as a percentage of the watershed.Surface water sampling was performed three times for each lake during the period of greatest flow (May-August 2001-2005). Nutrient and algal community data were determined as summer averages for the upper mixed zone at the deepest point in each lake. Si was determined as dissolved silicate, and DIN was determined as the sum of nitrite (NO<sub>2</sub><sup>-</sup>), nitrate (NO<sub>3</sub><sup>-</sup>), ammonia (NH<sub>3</sub>) and ammonium (NH<sub>4</sub><sup>+</sup>) using standard methods (Eaton et al. 1998) and second derivative spectroscopy (Crumpton et al. 1992) for NO<sub>2</sub><sup>-</sup> and NO<sub>3</sub><sup>-</sup>. We estimated the fraction of the phytoplankton composed of diatoms in each lake by sampling on the same days as water chemistry samples were extracted, then settling, identifying, and measuring biomasses of plankton in subsamples by standard methods (Hillebrand et al. 1999). In lakes we have studied year-round, we found no spring bloom of diatoms, and our samples were taken during the time of year when maximal phytoplankton biomass is expected. Therefore, our diatom analyses reflect the composition during the period when diatom sedimentation is most likely. <b>Geographical analysis.</b> Watershed boundaries and areas under agricultural land uses were analyzed using GIS of the temporally closest available digital coverages (2002), 30 meter resolution, Landsat 5 TM imagery. Land cover types were according the the National Land Cover Database (2001; Homer et al. 2007). The total agricultural land in the watershed was considered to be the sum of maize and soybean land use, the land area in grazed and ungrazed grasslands, “other agriculture”, alfalfa, winter wheat, lush grass, conservation reserve lands, and barren lands, since all of these lands are usually used for cropping or pastureland in this region. The area of the watersheds and the lakes were measured from the same GIS layers in order to estimate the potential for hydraulic flushing of the lake basins.