cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8091041
title: Schrey et al Kenya house sparrow invasion Msat data.xlsx

description: Microsatellite genotypes among Kenya house sparrows
DOI: 10.6084/m9.figshare.8091041.v1
title: Schrey et al Kenya house sparrow invasion Msat data.xlsx

description: Microsatellite genotypes among Kenya house sparrows
DOI: 10.6084/m9.figshare.8090852
title: Wilson et al 2019_DBA data.xlsx

description: Data associated with the paper "Estimates for energy expenditure in free-living animals using acceleration proxies; a reappraisal", accepted for publication in the Journal of Animal Ecology in 2019.
DOI: 10.6084/m9.figshare.8089685
title: Colour change and behavioural choice facilitate chameleon prawn camouflage against different seaweed backgrounds - Supplementary Data

description: Supplementary data from the accepted manuscript: Green SD, Duarte RC, Kellet E, Alagaratnam N & Stevens M. Colour change and behavioural choice facilitate chameleon prawn camouflage against different seaweed backgrounds. Communications Biology. 2019.<br>The uploaded file contains (i) camouflage data (expressed as JND) for wild chameleon prawns in the vision of both pollack and goby fish; (ii) results of the colour change experiment of green and red prawn types maintained in the seaweeds red dulse and green sea lettuce, respectively; (iii) results of the behavioural choice experiment testing the seaweed preference of green and red prawn types.
DOI: 10.6084/m9.figshare.8089685.v1
title: Colour change and behavioural choice facilitate chameleon prawn camouflage against different seaweed backgrounds - Supplementary Data

description: Supplementary data from the accepted manuscript: Green SD, Duarte RC, Kellet E, Alagaratnam N & Stevens M. Colour change and behavioural choice facilitate chameleon prawn camouflage against different seaweed backgrounds. Communications Biology. 2019.<br>The uploaded file contains (i) camouflage data (expressed as JND) for wild chameleon prawns in the vision of both pollack and goby fish; (ii) results of the colour change experiment of green and red prawn types maintained in the seaweeds red dulse and green sea lettuce, respectively; (iii) results of the behavioural choice experiment testing the seaweed preference of green and red prawn types.
DOI: 10.6084/m9.figshare.8089397
title: LSHTM RCUK Open Access Block Grant Compliance Report 2018-19

description: LSHTM RCUK Open Access Block Grant Compliance Report 2018-19<br>
DOI: 10.6084/m9.figshare.8089397.v1
title: LSHTM RCUK Open Access Block Grant Compliance Report 2018-19

description: LSHTM RCUK Open Access Block Grant Compliance Report 2018-19<br>
DOI: 10.6084/m9.figshare.8089220
title: Supporting data: Keeping cool in the heat: Behavioral thermoregulation and body temperature patterns in wild vervet monkeys

description: Data and R code in support of manuscript
DOI: 10.6084/m9.figshare.8089214
title: AM.nc

description: AM reconstruction NetCDF file.<br>
DOI: 10.6084/m9.figshare.8089142
title: RAW_DATAs_PloS.xlsx

description: Raw datas for all variables
DOI: 10.6084/m9.figshare.8089148
title: Garcia_Austrolebias

description: Primary data for conclusions in García et al., Freshwater Biology, 2019
DOI: 10.6084/m9.figshare.8089214.v1
title: AM.nc

description: AM reconstruction NetCDF file.<br>
DOI: 10.6084/m9.figshare.8089049
title: High-fat diet in pregnant rats and adverse fetal outcome

description: <b>Background:</b> Although pregestational obesity has been associated with increased risk of adverse fetal outcome, the mechanisms behind are not known. We aimed to investigate the influence of the maternal metabolic state on fetal outcome in rats exposed to either a high-fat diet (HFD) or a control diet (CD). We also investigated the impact of serum collected from HFD/CD pregnant rats on CD embryonic development in whole-embryo cultures. <b>Material and methods:</b> On gestational day 0, 9, 10, or 20 maternal plasma/serum samples were collected as pregnancies were terminated for the estimations of maternal metabolic state and embryo-fetal development. We measured embryonic gene expression of ROS scavenger enzymes as well as genes involved in inflammation in maternal adipose tissue. <b>Results:</b> In HFD maternal plasma/serum, concentrations of glucose, β-hydroxybutyrate, branched-chain amino acids, and leptin were increased, whereas those of triacylglycerol, cholesterol, and palmitic, oleic, linoleic, and α-linolenic acids were decreased. Gene expression of CuZnSOD, IL-6, IL-10, and resistin was increased in HFD maternal adipose tissue, whereas that of CuZnSOD and MnSOD was decreased in HFD-exposed embryos. HFD caused retention of most fatty acids in the maternal liver as well. <b>Conclusion:</b> HFD alters the maternal metabolic state, increases fetal resorptions <i>in vivo</i>, and increases the rate of fetal/embryonic malformations both <i>in vivo</i> and <i>in vitro</i>. These findings suggest that metabolic disturbances in HFD pregnant rats have profound adverse developmental effects in the offspring.
DOI: 10.6084/m9.figshare.8088995
title: datasets.csv

description: This Database belongs to “A Database for Using Machine Learning and Data Mining Techniques for Coronary Artery Disease diagnosis” research paper. This database includes 15 tables. We chose to index papers related to CAD detection using machine learning and data mining approaches that are published between 1992 and 2018. These criteria result in 126 papers in which 490 authors contributed to these papers. These papers studied 68 different datasets with almost more than 360 distinct features collected in 18 countries from Asia, Europe, and America. In these papers, 140 different machine learning or data mining techniques were applied to diagnose CAD. To use csv file, open it in excel or import it in your database.
DOI: 10.6084/m9.figshare.8089049.v1
title: High-fat diet in pregnant rats and adverse fetal outcome

description: <b>Background:</b> Although pregestational obesity has been associated with increased risk of adverse fetal outcome, the mechanisms behind are not known. We aimed to investigate the influence of the maternal metabolic state on fetal outcome in rats exposed to either a high-fat diet (HFD) or a control diet (CD). We also investigated the impact of serum collected from HFD/CD pregnant rats on CD embryonic development in whole-embryo cultures. <b>Material and methods:</b> On gestational day 0, 9, 10, or 20 maternal plasma/serum samples were collected as pregnancies were terminated for the estimations of maternal metabolic state and embryo-fetal development. We measured embryonic gene expression of ROS scavenger enzymes as well as genes involved in inflammation in maternal adipose tissue. <b>Results:</b> In HFD maternal plasma/serum, concentrations of glucose, β-hydroxybutyrate, branched-chain amino acids, and leptin were increased, whereas those of triacylglycerol, cholesterol, and palmitic, oleic, linoleic, and α-linolenic acids were decreased. Gene expression of CuZnSOD, IL-6, IL-10, and resistin was increased in HFD maternal adipose tissue, whereas that of CuZnSOD and MnSOD was decreased in HFD-exposed embryos. HFD caused retention of most fatty acids in the maternal liver as well. <b>Conclusion:</b> HFD alters the maternal metabolic state, increases fetal resorptions <i>in vivo</i>, and increases the rate of fetal/embryonic malformations both <i>in vivo</i> and <i>in vitro</i>. These findings suggest that metabolic disturbances in HFD pregnant rats have profound adverse developmental effects in the offspring.
DOI: 10.6084/m9.figshare.8088890
title: Authors.csv

description: This Database belongs to “A Database for Using Machine Learning and Data Mining Techniques for Coronary Artery Disease diagnosis” research paper. This database includes 15 tables. We chose to index papers related to CAD detection using machine learning and data mining approaches that are published between 1992 and 2018. These criteria result in 126 papers in which 490 authors contributed to these papers. These papers studied 68 different datasets with almost more than 360 distinct features collected in 18 countries from Asia, Europe, and America. In these papers, 140 different machine learning or data mining techniques were applied to diagnose CAD. To use csv file, open it in excel or import it in your database.
DOI: 10.6084/m9.figshare.8088857
title: DA.nc

description: DA reconstruction NetCDF file<br>
DOI: 10.6084/m9.figshare.8088881
title: Blume-Werry_et_al_Dwelling in the deep_data and statistics script

description: for details see publication in New Phytologist: Blume-Werry et al. 2019 Dwelling in the deep - strongly increased root growth and rooting depth enhance plant interactions with thawing permafrost<br>
DOI: 10.6084/m9.figshare.8088995.v2
title: datasets

description: This Database belongs to “A Database for Using Machine Learning and Data Mining Techniques for Coronary Artery Disease diagnosis” research paper. This database includes 15 tables. We chose to index papers related to CAD detection using machine learning and data mining approaches that are published between 1992 and 2018. These criteria result in 126 papers in which 490 authors contributed to these papers. These papers studied 68 different datasets with almost more than 360 distinct features collected in 18 countries from Asia, Europe, and America. In these papers, 140 different machine learning or data mining techniques were applied to diagnose CAD. To use csv file, open it in excel or import it in your database.
DOI: 10.6084/m9.figshare.8088848
title: Supplemental Table S1-7

description: Supplemental Table S1. Primers for miRNAsQ-PCR.<br>Supplemental Table S2. Clean reads mapped results.Supplemental Table S3. Identification of conserved miRNAs in six libraries.Supplemental Table S4. Identification of novel miRNAs in pigeon gonads.Supplemental Table S5. The basic expression data of predicted miRNAs.Supplemental Table S6. The list of predicted multiple miRNAs target genes.Supplemental Table S7. The list of enrichment GO analysis.
DOI: 10.6084/m9.figshare.8088881.v2
title: Blume-Werry_et_al_Dwelling in the deep_data and statistics script

description: for details see publication in New Phytologist: Blume-Werry et al. 2019 Dwelling in the deep - strongly increased root growth and rooting depth enhance plant interactions with thawing permafrost<br>
DOI: 10.6084/m9.figshare.8088848.v1
title: Supplemental Table S1-7

description: Supplemental Table S1. Primers for miRNAsQ-PCR.<br>Supplemental Table S2. Clean reads mapped results.Supplemental Table S3. Identification of conserved miRNAs in six libraries.Supplemental Table S4. Identification of novel miRNAs in pigeon gonads.Supplemental Table S5. The basic expression data of predicted miRNAs.Supplemental Table S6. The list of predicted multiple miRNAs target genes.Supplemental Table S7. The list of enrichment GO analysis.
DOI: 10.6084/m9.figshare.8088857.v1
title: DA.nc

description: DA reconstruction NetCDF file<br>
DOI: 10.6084/m9.figshare.8088881.v1
title: data and statistics script

description: for details see publication in New Phytologist<br>
DOI: 10.6084/m9.figshare.8088674
title: Group A streptococcal M-protein specific antibodies and T-cells drive the pathology observed in the rat autoimmune valvulitis model

description: Acute rheumatic fever (ARF) and rheumatic heart disease (RHD) are autoimmune mediated diseases triggered by group A streptococcal (GAS) infections. Molecular mimicry between GAS M-proteins and host tissue proteins has been proposed as the mechanism that initiates autoreactive immune responses in ARF/RHD. However, the individual role of antibodies and T-cells specific for GAS M-proteins in the pathogenesis of autoimmune carditis remains under-explored. The current study investigated the role of antibodies and T-cells in the development of carditis in the Lewis rat autoimmune valvultis (RAV) model by transferring serum and/or splenic T-cells from rats previously injected with GAS recombinant M5 protein. Here we report that serum antibodies alone and serum plus <i>in vitro</i> expanded rM5-specific T-cells from hyperimmune rats were capable of transferring carditis to naïve syngeneic animals. Moreover, the rats that received combined serum and T-cells developed more severe carditis. Recipient rats developed mitral valvulitis and myocarditis and showed prolongation of P-R intervals in electrocardiography. GAS M5 protein-specific IgG reactivity and T-cell recall response were also demonstrated in recipient rats indicating long-term persistence of antibodies and T-cells following transfer. The results suggest that both anti-GAS M5 antibodies and T-cells have differential propensity to induce autoimmune mediated carditis in syngeneic rats following transfer. The results highlight that antibodies and effector T-cells generated by GAS M protein injection can also independently home into cardiac tissue to cross-react with tissue proteins causing autoimmune mediated immunopathology.
DOI: 10.6084/m9.figshare.8088647
title: Epigenome-wide DNA methylation in placentas from preterm infants: association with maternal socioeconomic status

description: This study evaluated the hypothesis that prenatal maternal socioeconomic status (SES) adversity is associated with DNA methylation in the placenta. SES adversity was defined by the presence of, as well as a summative count of, four factors: less than college education, single marital status, food and nutritional service assistance, and public health insurance. Epigenome-wide DNA methylation was assessed using the Illumina EPIC array in 426 placentas from a sample of infants born &lt; 28 weeks of gestation from the Extremely Low Gestational Age Newborn cohort. Associations between SES adversity and DNA methylation were assessed with robust linear regressions adjusted for covariates and controlled the false discovery rate at &lt; 10%. We also examined whether such associations were sex specific. Indicators of SES adversity were associated with differential methylation at 33 CpG sites. Of the 33 identified CpG sites, 19 (57.6%) displayed increased methylation, and 14 (42.4%) displayed decreased methylation in association with at least one of the SES adversity factors. Sex differences were observed in DNA methylation associated with summative SES score; in which placentas derived from female pregnancies showed more robust differential CpG methylation than placentas from male pregnancies. Maternal SES adversity was associated with differential methylation of genes with key role in gene transcription and placental function, potentially altering immunity and stress response. Further investigation is needed to evaluate the role of epigenetic differences in mediating the association between maternal socioeconomic status during pregnancy and later life health outcomes in children.
DOI: 10.6084/m9.figshare.8088674.v1
title: Group A streptococcal M-protein specific antibodies and T-cells drive the pathology observed in the rat autoimmune valvulitis model

description: Acute rheumatic fever (ARF) and rheumatic heart disease (RHD) are autoimmune mediated diseases triggered by group A streptococcal (GAS) infections. Molecular mimicry between GAS M-proteins and host tissue proteins has been proposed as the mechanism that initiates autoreactive immune responses in ARF/RHD. However, the individual role of antibodies and T-cells specific for GAS M-proteins in the pathogenesis of autoimmune carditis remains under-explored. The current study investigated the role of antibodies and T-cells in the development of carditis in the Lewis rat autoimmune valvultis (RAV) model by transferring serum and/or splenic T-cells from rats previously injected with GAS recombinant M5 protein. Here we report that serum antibodies alone and serum plus <i>in vitro</i> expanded rM5-specific T-cells from hyperimmune rats were capable of transferring carditis to naïve syngeneic animals. Moreover, the rats that received combined serum and T-cells developed more severe carditis. Recipient rats developed mitral valvulitis and myocarditis and showed prolongation of P-R intervals in electrocardiography. GAS M5 protein-specific IgG reactivity and T-cell recall response were also demonstrated in recipient rats indicating long-term persistence of antibodies and T-cells following transfer. The results suggest that both anti-GAS M5 antibodies and T-cells have differential propensity to induce autoimmune mediated carditis in syngeneic rats following transfer. The results highlight that antibodies and effector T-cells generated by GAS M protein injection can also independently home into cardiac tissue to cross-react with tissue proteins causing autoimmune mediated immunopathology.
DOI: 10.6084/m9.figshare.8088647.v2
title: Epigenome-wide DNA methylation in placentas from preterm infants: association with maternal socioeconomic status

description: This study evaluated the hypothesis that prenatal maternal socioeconomic status (SES) adversity is associated with DNA methylation in the placenta. SES adversity was defined by the presence of, as well as a summative count of, four factors: less than college education, single marital status, food and nutritional service assistance, and public health insurance. Epigenome-wide DNA methylation was assessed using the Illumina EPIC array in 426 placentas from a sample of infants born &lt; 28 weeks of gestation from the Extremely Low Gestational Age Newborn cohort. Associations between SES adversity and DNA methylation were assessed with robust linear regressions adjusted for covariates and controlled the false discovery rate at &lt; 10%. We also examined whether such associations were sex specific. Indicators of SES adversity were associated with differential methylation at 33 CpG sites. Of the 33 identified CpG sites, 19 (57.6%) displayed increased methylation, and 14 (42.4%) displayed decreased methylation in association with at least one of the SES adversity factors. Sex differences were observed in DNA methylation associated with summative SES score; in which placentas derived from female pregnancies showed more robust differential CpG methylation than placentas from male pregnancies. Maternal SES adversity was associated with differential methylation of genes with key role in gene transcription and placental function, potentially altering immunity and stress response. Further investigation is needed to evaluate the role of epigenetic differences in mediating the association between maternal socioeconomic status during pregnancy and later life health outcomes in children.
DOI: 10.6084/m9.figshare.8088647.v1
title: Epigenome-Wide DNA Methylation in Placentas from Preterm Infants: Association with Maternal Socioeconomic Status

description: This study evaluated the hypothesis that prenatal maternal socioeconomic status (SES) adversity is associated with DNA methylation in the placenta. SES adversity was defined by the presence of, as well as a summative count of, the these factors: less than college education, single marital status, food and nutritional service assistance, and public health insurance. Epigenome-wide DNA methylation was assessed using the Illumina EPIC array in 426 placentas from a sample of infants born &lt; 28 weeks of gestation from the Extremely Low Gestational Age Newborn cohort. Associations between SES adversity and DNA methylation were assessed with robust linear regressions adjusted for covariates and controlled the false discovery rate at &lt; 10%. We also examined whether such associations were sex-specific. Indicators of SES adversity were associated with differential methylation at 33 CpG sites. Of the 33 identified CpG sites, 19 (57.6%) displayed increased methylation, and 14 (42.4%) displayed decreased methylation in association with at least one of the socioeconomic adversity factors. Sex differences were observed in DNA methylation associated with summative SES score; in which placentas derived from female pregnancies showed more robust differential CpG methylation than placentas from male pregnancies. Maternal SES adversity was associated with differential methylation of genes with key role in gene transcription and placental function, potentially altering immunity and stress response. Further investigation is needed to evaluate the role of epigenetic differences in mediating the association between maternal socioeconomic status during pregnancy and later life health outcomes in children.
DOI: 10.6084/m9.figshare.8088617
title: siEMSY protein list_detected in N=4.xlsx

description: Processed global mass spec proteomics data from siRNA knockdown of EMSY in skin organoid<br>
DOI: 10.6084/m9.figshare.8088611
title: siEMSY protein list_all detected proteins.xlsx

description: Processed global mass spec proteomics data from siRNA knockdown of EMSY in skin organoid
DOI: 10.6084/m9.figshare.8088617.v1
title: siEMSY protein list_detected in N=4.xlsx

description: Processed global mass spec proteomics data from siRNA knockdown of EMSY in skin organoid<br>
DOI: 10.6084/m9.figshare.8088578
title: Results from a meta-analysis of defence priming by organismal and non-organismal agents in Arabidopsis Thaliana

description: This dataset contains the findings from a meta-analysis of defence priming in <i>Arabidopsis thaliana</i> from 267 experiments across 77 papers. Data are provided as a semicolon delimited CSV file.<br>Plant resistance to biotic stressors can be strengthened by priming the defence response with organismal and non-organismal agents. Stimulation with such agents triggers a minor part of the plant defence response that confers greater speed, strength and/or endurance against subsequent threats. This defence priming of plants could enhance the protection of crops against pests and diseases while reducing the use of agrochemicals.<br>This dataset presents aggregated effect size values resulting from defence priming with numerous agents and subsequent biotic stressors. Responses quantified in the recorded experiments include lesion area, feeding damage, bacterial growth, infection, disease severity, spore production, feeding duration, population increase, herbivore weight, time to pupation and/or reproduction rate. <br>The following data are included in <b>Westman priming rawdata.csv</b> for each experiment:<br><b>First Author</b> - First author of the associated paper<b>Year </b>- Publication year of the associated paper<b>Ecotype </b>- Ecotype of <i>A. thaliana</i> studied<b>Priming agent</b> - Priming agent studied<b>Biotic stress</b> - Biotic stress the response to which was studied<b>Nr of times repeated</b> - Number of times the experiment was repeated in the given study<b>nT </b>- n of treatment group<b>nC </b>- n of control group <b>m1T </b>- Treatment group mean for quantified response<b>m1C </b>- Control group mean for quantified response<b>sd1T </b>- Treatment group standard deviation<b>sd1C </b>- Control group standard deviation<b>g </b>- Effect size, given as Hedge's g<b>var.g </b>- Variance of g<b>Priming_class_Broad</b> - Broad classification of the priming agent<b>Triggering_class_broad </b>- Broad classification of the biotic stressor<br>
DOI: 10.6084/m9.figshare.8088590
title: Pentraxin 3 regulates neutrophil infiltration to the brain during neuroinflammation

description: Data set for <b>:<br><br>Pentraxin 3 regulates neutrophil infiltration to the brain during neuroinflammation</b>
DOI: 10.6084/m9.figshare.8088590.v1
title: Pentraxin 3 regulates neutrophil infiltration to the brain during neuroinflammation

description: Data set for <b>:<br><br>Pentraxin 3 regulates neutrophil infiltration to the brain during neuroinflammation</b>