cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5334373
title: Drought tolerance induced by sound in Arabidopsis plants

description: We examined the responses of sound-treated arabidopsis adult plants to water deprivation and the associated changes on gene expression. The survival of drought-induced plants was significantly higher in the sound treated plants (24,8%) compared with plants kept in silence (13,3%). RNA-seq revealed significant upregulation of 87 genes including 32 genes involved in abiotic stress responses, 31 involved in pathogen responses, 11 involved in oxidation-reduction processes, 5 involved in the regulation of transcription, 2 genes involved in protein phosphorylation/dephosphorylation and 13 involved in jasmonic acid or ethylene synthesis or responses. In addition, 2 genes involved in the responses to mechanical stimulus were also induced by sound, suggesting that touch and sound have at least partially common perception and signaling events.
DOI: 10.6084/m9.figshare.5334373.v1
title: Drought tolerance induced by sound in Arabidopsis plants

description: We examined the responses of sound-treated arabidopsis adult plants to water deprivation and the associated changes on gene expression. The survival of drought-induced plants was significantly higher in the sound treated plants (24,8%) compared with plants kept in silence (13,3%). RNA-seq revealed significant upregulation of 87 genes including 32 genes involved in abiotic stress responses, 31 involved in pathogen responses, 11 involved in oxidation-reduction processes, 5 involved in the regulation of transcription, 2 genes involved in protein phosphorylation/dephosphorylation and 13 involved in jasmonic acid or ethylene synthesis or responses. In addition, 2 genes involved in the responses to mechanical stimulus were also induced by sound, suggesting that touch and sound have at least partially common perception and signaling events.
DOI: 10.6084/m9.figshare.5334142
title: High-throughput DFT calculations of formation energy, stability and oxygen vacancy formation energy of ABO3 perovskites

description: ABO<sub>3</sub> perovskites are oxide materials that are used for a variety of applications such as solid oxide fuel cells, piezo-, ferro-electricity and water splitting. Due to their remarkable stability with respect to cation substitution, new compounds for such applications potentially await discovery. In this work, we present an exhaustive dataset of formation energies of 5,329 cubic and distorted perovskites that were calculated using first-principles density functional theory. In addition to formation energies, several additional properties such as oxidation states, band gap, oxygen vacancy formation energy, and thermodynamic stability with respect to all phases in the Open Quantum Materials Database are also made publicly available. This large dataset for this ubiquitous crystal structure type contains 395 perovskites that are predicted to be thermodynamically stable, of which many have not yet been experimentally reported, and therefore represent theoretical predictions. The dataset thus opens avenues for future use, including materials discovery in many research-active areas.
DOI: 10.6084/m9.figshare.5334049
title: XML

description: BEAST XML files for the 200 models
DOI: 10.6084/m9.figshare.5334037
title: FASTA Alignments

description: 50 pre-discrete and 50 post-discrete FASTA alignments of the subsampled 2014-15 influenza A/H3N2 season in the U.S.
DOI: 10.6084/m9.figshare.5334034
title: All 512 pathogenic or likely pathogenic variants detected in 410 patients

description: Table S3 from "Proband-only Medical Exome Sequencing as a Cost-effective First-tier Genetic Diagnostic Test for Patients Without Prior Molecular Tests and Clinical Diagnosis in a Developing Country: the China Experience" on Genetics in Medicine<br><b></b>
DOI: 10.6084/m9.figshare.5334049.v1
title: XML

description: BEAST XML files for the 200 models
DOI: 10.6084/m9.figshare.5334034.v1
title: All 512 pathogenic or likely pathogenic variants detected in 410 patients

description: Table S3 from "Proband-only Medical Exome Sequencing as a Cost-effective First-tier Genetic Diagnostic Test for Patients Without Prior Molecular Tests and Clinical Diagnosis in a Developing Country: the China Experience" on Genetics in Medicine<br><b></b>
DOI: 10.6084/m9.figshare.5332240
title: ELISPOTS

description: ELISpots data for specific plasma cells against influenza viruses
DOI: 10.6084/m9.figshare.5332258
title: Thesis Files

description: Full-text, test data, pictures, Excel and MATLAB analysis files, and manufacturing photographs for further analysis of the results.<br>
DOI: 10.6084/m9.figshare.5332888
title: Pellet dispenser assembly files

description: Supplementary files described in the paper:<br> *Abel Torres-Espín, *Juan Forero, Emma Schmidt, Karim Fouad, Keith K. Fenrich (2017) A motorized pellet dispenser to deliver high intensity training of the single pellet task in rats. Behavioural Brain Research (<i>*co-lead author</i>).<br>
DOI: 10.6084/m9.figshare.5332888.v1
title: Pellet dispenser assembly files

description: Supplementary files described in the paper:<br> *Abel Torres-Espín, *Juan Forero, Emma Schmidt, Karim Fouad, Keith K. Fenrich (2017) A motorized pellet dispenser to deliver high intensity training of the single pellet task in rats. Behavioural Brain Research (<i>*co-lead author</i>).<br>
DOI: 10.6084/m9.figshare.5332189
title: Non-targeted workflow for identification of antimicrobial compounds in animal feed using bioassay-directed screening in combination with liquid chromatography-high resolution mass spectrometry

description: A non-targeted workflow is reported for the isolation and identification of antimicrobial active compounds using bioassay-directed screening and LC coupled to high-resolution MS. Suspect samples are extracted using a generic protocol and fractionated using two different LC conditions (A and B). The behaviour of the bioactive compound under these different conditions yields information about the physicochemical properties of the compound and introduces variations in co-eluting compounds in the fractions, which is essential for peak picking and identification. The fractions containing the active compound(s) obtained with conditions A and B are selected using a microbiological effect-based bioassay. The selected bioactive fractions from A and B are analysed using LC combined with high-resolution MS. Selection of relevant signals is automatically carried out by selecting all signals present in both bioactive fractions A and B, yielding tremendous data reduction. The method was assessed using two spiked feed samples and subsequently applied to two feed samples containing an unidentified compound showing microbial growth inhibition. In all cases, the identity of the compound causing microbiological inhibition was successfully confirmed.
DOI: 10.6084/m9.figshare.5332258.v1
title: Project Files

description: Test data and pictures, Excel and MATLAB analysis files and manufacturing photographs for further analysis of the results.<br>
DOI: 10.6084/m9.figshare.5332186
title: Mouse vaccination data

description: Mice data of comparison of infection vs vaccination in pff and nb
DOI: 10.6084/m9.figshare.5332189.v1
title: Non-targeted workflow for identification of antimicrobial compounds in animal feed using bioassay-directed screening in combination with liquid chromatography-high resolution mass spectrometry

description: A non-targeted workflow is reported for the isolation and identification of antimicrobial active compounds using bioassay-directed screening and LC coupled to high-resolution MS. Suspect samples are extracted using a generic protocol and fractionated using two different LC conditions (A and B). The behaviour of the bioactive compound under these different conditions yields information about the physicochemical properties of the compound and introduces variations in co-eluting compounds in the fractions, which is essential for peak picking and identification. The fractions containing the active compound(s) obtained with conditions A and B are selected using a microbiological effect-based bioassay. The selected bioactive fractions from A and B are analysed using LC combined with high-resolution MS. Selection of relevant signals is automatically carried out by selecting all signals present in both bioactive fractions A and B, yielding tremendous data reduction. The method was assessed using two spiked feed samples and subsequently applied to two feed samples containing an unidentified compound showing microbial growth inhibition. In all cases, the identity of the compound causing microbiological inhibition was successfully confirmed.
DOI: 10.6084/m9.figshare.5332156
title: Inv FUT.xlsx

description: paper...
DOI: 10.6084/m9.figshare.5332258.v3
title: Thesis Files

description: Full-text, test data, pictures, Excel and MATLAB analysis files, and manufacturing photographs for further analysis of the results.<br>
DOI: 10.6084/m9.figshare.5332111
title: Ferret antiserum data

description: cross-reactivity induced by infection vs vaccination with rHA proteins.
DOI: 10.6084/m9.figshare.5332156.v1
title: Inv FUT.xlsx

description: paper...
DOI: 10.6084/m9.figshare.5332258.v2
title: THESIS: Open-hole tensile strength and size effect of CFR polymers: an anisotropic approach

description: Test data and pictures, Excel and MATLAB analysis files and manufacturing photographs for further analysis of the results.<br>
DOI: 10.6084/m9.figshare.5332111.v1
title: Ferret antiserum data

description: cross-reactivity induced by infection vs vaccination with rHA proteins.
DOI: 10.6084/m9.figshare.5331949
title: A new species of <i>Varanus</i> (Anguimorpha: Varanidae) from the early Miocene of the Czech Republic, and its relationships and palaeoecology

description: Skeletal remains of a new early Miocene (Ottnangian, MN 4 mammal zone) monitor lizard, <i>Varanus mokrensis</i> sp. nov., are described from two karst fissures in the Mokrá-Western Quarry (1/2001 Turtle Joint; 2/2003 Reptile Joint), Czech Republic, providing the first documented example of a European varanid for which osteological data permit a well-supported assignment to the genus <i>Varanus</i>. The new species is morphologically similar to the Recent Indo-Asiatic varanids of the <i>Varanus bengalensis</i> group. It differs from all other <i>Varanus</i> species on the basis of a single autapomorphy and a combination of 11 characters. As a distinguishing feature of <i>V. mokrensis</i>, the parietal and squamosal processes of the postorbitofrontal form a narrowly acute angle. The teeth show distinct, smooth cutting edges along the mesial and distal margins of the apical portion of their crowns. This feature is not observed in most extant Asiatic <i>Varanus</i> species and may represent a plesiomorphic condition. The results of parsimony phylogenetic analyses, with and without character reweighting, reveal poor resolution within <i>Varanus</i>. A Bayesian analysis shows <i>V. mokrensis</i> to be closely related to extant representatives of the Indo-Asiatic <i>Varanus</i> clade, with close affinities to the <i>V. bengalensis</i> species group. The topology of the Bayesian tree supports the hypothesis that Miocene monitors from Mokrá are representatives of a lineage that is ancestral to the well-defined clade of extant African varanids, including the early Miocene <i>V. rusingensis</i>. In addition, our results support a Eurasian origin for the varanid clade. The extant African <i>Varanus</i> species probably originated in the late Oligocene. The radiation of African varanids probably occurred during the late Oligocene to early Miocene time interval. The occurrence of <i>Varanus</i> in the early Miocene of Mokrá-Western Quarry corresponds to the warm phase of the Miocene Climatic Optimum. Remains of a diverse aquatic and heliophobe amphibian fauna at the 2/2003 Reptile Joint site indicate more humid conditions than those at the 1/2001 Turtle Joint site. http://zoobank.org/urn:lsid:zoobank.org:pub:B1553295-8AC7-42F0-91C4-51C4C13F1C9D
DOI: 10.6084/m9.figshare.5331949.v1
title: A new species of <i>Varanus</i> (Anguimorpha: Varanidae) from the early Miocene of the Czech Republic, and its relationships and palaeoecology

description: Skeletal remains of a new early Miocene (Ottnangian, MN 4 mammal zone) monitor lizard, <i>Varanus mokrensis</i> sp. nov., are described from two karst fissures in the Mokrá-Western Quarry (1/2001 Turtle Joint; 2/2003 Reptile Joint), Czech Republic, providing the first documented example of a European varanid for which osteological data permit a well-supported assignment to the genus <i>Varanus</i>. The new species is morphologically similar to the Recent Indo-Asiatic varanids of the <i>Varanus bengalensis</i> group. It differs from all other <i>Varanus</i> species on the basis of a single autapomorphy and a combination of 11 characters. As a distinguishing feature of <i>V. mokrensis</i>, the parietal and squamosal processes of the postorbitofrontal form a narrowly acute angle. The teeth show distinct, smooth cutting edges along the mesial and distal margins of the apical portion of their crowns. This feature is not observed in most extant Asiatic <i>Varanus</i> species and may represent a plesiomorphic condition. The results of parsimony phylogenetic analyses, with and without character reweighting, reveal poor resolution within <i>Varanus</i>. A Bayesian analysis shows <i>V. mokrensis</i> to be closely related to extant representatives of the Indo-Asiatic <i>Varanus</i> clade, with close affinities to the <i>V. bengalensis</i> species group. The topology of the Bayesian tree supports the hypothesis that Miocene monitors from Mokrá are representatives of a lineage that is ancestral to the well-defined clade of extant African varanids, including the early Miocene <i>V. rusingensis</i>. In addition, our results support a Eurasian origin for the varanid clade. The extant African <i>Varanus</i> species probably originated in the late Oligocene. The radiation of African varanids probably occurred during the late Oligocene to early Miocene time interval. The occurrence of <i>Varanus</i> in the early Miocene of Mokrá-Western Quarry corresponds to the warm phase of the Miocene Climatic Optimum. Remains of a diverse aquatic and heliophobe amphibian fauna at the 2/2003 Reptile Joint site indicate more humid conditions than those at the 1/2001 Turtle Joint site. http://zoobank.org/urn:lsid:zoobank.org:pub:B1553295-8AC7-42F0-91C4-51C4C13F1C9D
DOI: 10.6084/m9.figshare.5331934
title: Dataset for: Effect of Densely Ionizing Radiation on Cardiomyocyte Differentiation from Human Induced Pluripotent Stem Cells

description: The process of human cardiac development can be faithfully recapitulated in a culture dish with human pluripotent stem cells, where the impact of environmental stressors can be evaluated. The consequences of ionizing radiation exposure on human cardiac differentiation are largely unknown. In this study, human induced pluripotent stem cell cultures (hiPSCs) were subjected to an external beam of 3.7 MeV α-particles at low mean absorbed doses of 0.5, 3 and 10 cGy. Subsequently, the hiPSCs were differentiated into beating cardiac myocytes (hiPSC-CMs). Pluripotent and cardiac markers and morphology did not reveal differences between the irradiated and non-irradiated groups. While cell number was not affected during CM differentiation, cell number of differentiated CMs was severely reduced by ionizing radiation in a dose-responsive manner. β-adrenergic stimulation causes calcium (Ca2+) overload and oxidative stress. Although no significant increase in Ca2+ transient amplitude was observed in any group after treatment with 1 µM isoproterenol, the incidence of spontaneous Ca2+ waves/releases was more frequent in hiPSC-CMs of the irradiated groups, indicating arrhythmogenic activities at the single cell level. Increased transcript expression of mitochondrial biomarkers (LONP1, TFAM) and mtDNA-encoded genes (MT-CYB, MT-RNR1) was detected upon differentiation of hiPSC-CMs suggesting increased organelle biogenesis. Exposure of hiPSC-CM cultures to 10 cGy significantly upregulated MT-CYB and MT-RNR1 expression, which may reflect an adaptive response to ionizing radiation. Our results indicate that important aspects of differentiation of hiPSCs into cardiac myocytes may be affected by low fluences of densely ionizing radiations such as α-particles.
DOI: 10.6084/m9.figshare.5331892
title: An Exercise in Spatial Modelling: The Minoan Aegean

description: These are files used to give a one hour exercise in spatial modelling in an archaeological context, that of the 39 sites of the Minoan Aegean. This was part of The Connected Past workshop held in Bournemouth University, 22-23 August 2017.
DOI: 10.6084/m9.figshare.5331934.v1
title: Dataset for: Effect of Densely Ionizing Radiation on Cardiomyocyte Differentiation from Human Induced Pluripotent Stem Cells

description: The process of human cardiac development can be faithfully recapitulated in a culture dish with human pluripotent stem cells, where the impact of environmental stressors can be evaluated. The consequences of ionizing radiation exposure on human cardiac differentiation are largely unknown. In this study, human induced pluripotent stem cell cultures (hiPSCs) were subjected to an external beam of 3.7 MeV α-particles at low mean absorbed doses of 0.5, 3 and 10 cGy. Subsequently, the hiPSCs were differentiated into beating cardiac myocytes (hiPSC-CMs). Pluripotent and cardiac markers and morphology did not reveal differences between the irradiated and non-irradiated groups. While cell number was not affected during CM differentiation, cell number of differentiated CMs was severely reduced by ionizing radiation in a dose-responsive manner. β-adrenergic stimulation causes calcium (Ca2+) overload and oxidative stress. Although no significant increase in Ca2+ transient amplitude was observed in any group after treatment with 1 µM isoproterenol, the incidence of spontaneous Ca2+ waves/releases was more frequent in hiPSC-CMs of the irradiated groups, indicating arrhythmogenic activities at the single cell level. Increased transcript expression of mitochondrial biomarkers (LONP1, TFAM) and mtDNA-encoded genes (MT-CYB, MT-RNR1) was detected upon differentiation of hiPSC-CMs suggesting increased organelle biogenesis. Exposure of hiPSC-CM cultures to 10 cGy significantly upregulated MT-CYB and MT-RNR1 expression, which may reflect an adaptive response to ionizing radiation. Our results indicate that important aspects of differentiation of hiPSCs into cardiac myocytes may be affected by low fluences of densely ionizing radiations such as α-particles.
DOI: 10.6084/m9.figshare.5331892.v1
title: An Exercise in Spatial Modelling: The Minoan Aegean

description: These are files used to give a one hour exercise in spatial modelling in an archaeological context, that of the 39 sites of the Minoan Aegean. This was part of The Connected Past workshop held in Bournemouth University, 22-23 August 2017.
DOI: 10.6084/m9.figshare.5331895
title: Capturing Context-Related Change in Emotional Dynamics via Fixed Moderated Time Series Analysis

description: Much of recent affect research relies on intensive longitudinal studies to assess daily emotional experiences. The resulting data are analyzed with dynamic models to capture regulatory processes involved in emotional functioning. Daily contexts, however, are commonly ignored. This may not only result in biased parameter estimates and wrong conclusions, but also ignores the opportunity to investigate contextual effects on emotional dynamics. With fixed moderated time series analysis, we present an approach that resolves this problem by estimating context-dependent change in dynamic parameters in single-subject time series models. The approach examines parameter changes of known shape and thus addresses the problem of <i>observed</i> intra-individual heterogeneity (e.g., changes in emotional dynamics due to observed changes in daily stress). In comparison to existing approaches to <i>unobserved</i> heterogeneity, model estimation is facilitated and different forms of change can readily be accommodated. We demonstrate the approach's viability given relatively short time series by means of a simulation study. In addition, we present an empirical application, targeting the joint dynamics of affect and stress and how these co-vary with daily events. We discuss potentials and limitations of the approach and close with an outlook on the broader implications for understanding emotional adaption and development.
DOI: 10.6084/m9.figshare.5331895.v1
title: Capturing Context-Related Change in Emotional Dynamics via Fixed Moderated Time Series Analysis

description: Much of recent affect research relies on intensive longitudinal studies to assess daily emotional experiences. The resulting data are analyzed with dynamic models to capture regulatory processes involved in emotional functioning. Daily contexts, however, are commonly ignored. This may not only result in biased parameter estimates and wrong conclusions, but also ignores the opportunity to investigate contextual effects on emotional dynamics. With fixed moderated time series analysis, we present an approach that resolves this problem by estimating context-dependent change in dynamic parameters in single-subject time series models. The approach examines parameter changes of known shape and thus addresses the problem of <i>observed</i> intra-individual heterogeneity (e.g., changes in emotional dynamics due to observed changes in daily stress). In comparison to existing approaches to <i>unobserved</i> heterogeneity, model estimation is facilitated and different forms of change can readily be accommodated. We demonstrate the approach's viability given relatively short time series by means of a simulation study. In addition, we present an empirical application, targeting the joint dynamics of affect and stress and how these co-vary with daily events. We discuss potentials and limitations of the approach and close with an outlook on the broader implications for understanding emotional adaption and development.
DOI: 10.6084/m9.figshare.5331697
title: A novel form of stereo vision in the praying mantis: DATA

description: The data support the research described in the unpublished paper entitle: 'A novel form of stereo vision in the praying mantis'. The data are from experiments investigated stereopsis in mantises (<i>Sphodromantis lineola</i>) and humans in different experiments as detailed in the paper. The datafiles for the mantises detail the occurence and number of strikes in response to different disparity, correlation and motion conditions. The datafiles for the human participants detail their judgement of whether a 3D target was near or far in response to different disparity, correlation and motion conditions.
DOI: 10.15131/shef.data.5331730.v1
title: Confirmatory Factor Analysis split - Insomnia negative affect and paranoia

description: Our full dataset was randomly split in half, we conducted an exploratory factor analysis (EFA) on one half of the dataset and a confirmatory factor analysis (CFA) on the other. <br>This dataset represents the confirmatory factor analysis dataset and forms the basis of the CFA presented in the PLoS paper: Scott, A.J., Rowse, G. and Webb, T.L. (2017) A structural equation model of the relationship between insomnia, negative affect, and paranoid thinking. PLoS One, 12 (10). e0186233. DOI:10.1371/journal.pone.0186233
DOI: 10.15131/shef.data.5331739.v1
title: Exploratory Factor Analysis split - Insomnia negative affect and paranoia

description: Our full dataset was randomly split in half, we conducted an exploratory factor analysis (EFA) on one half of the dataset and a confirmatory factor analysis (CFA) on the other.<br>This dataset represents the exploratory factor analysis dataset and forms the basis of the EFA presented in the PLoS paper: Scott, A.J., Rowse, G. and Webb, T.L. (2017) A structural equation model of the relationship between insomnia, negative affect, and paranoid thinking. PLoS One, 12 (10). e0186233. DOI:10.1371/journal.pone.0186233