cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1152727
title: Marine microbial eukaryote transcriptomes

description: <strong>Overview</strong> This repository provides assemblies of a sub-set publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes. The raw data were generated by the Marine Microbial Eukaryote Transcriptome Sequencing Project (http://marinemicroeukaryotes.org/). This project provides its own set of assemblies (generated using the Abyss assembler). Since our work-flows are geared towards assemblies generated by the Trinity assembler, raw data were obtained from the following website http://marinemicroeukaryotes.org/ and assembled using Trinity (http://trinityrnaseq.sourceforge.net/) For our purposes the raw data were directly assembled using Trinity (see README for version number) using the default settings. Several species/strains were assembled using all available Illumina libraries combined (see README). The identifiers of the raw data are provided and culture conditions of the organisms can be retrieved from http://marinemicroeukaryotes.org/ using the MMETSP ID (see README for list). <strong>If you use these data please cite</strong> Keeling, P.J. et al., 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLoS Biology, 12:e1001889. Grabherr, M.G. et al., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29:644-652. <strong>Funding</strong> NSF Dimensions of Biodiversity Grant DEB-1046075
DOI: 10.6084/m9.figshare.1152723.v1
title: MVA BLAST results

description: Data supplement
DOI: 10.6084/m9.figshare.1152725.v1
title: Independent data set of occurrence points T. infestans and R. prolixus

description: Independent data set of occurence points of <em>R. prolixus</em> from Venezuela, and <em>T. infestans</em> from Argentina species.
DOI: 10.6084/m9.figshare.1152727.v1
title: Marine microbial eukaryote transcriptomes

description: Assemblies of publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes.
DOI: 10.6084/m9.figshare.1152691
title: List of journals that do not provide a publishing option compliant with the Trust

description: Using Sherpa FACT (http://www.sherpa.ac.uk/fact/) and our own repository of publisher correspondence, we undertook an analysis to determine which of the journals Wellcome Trust authors published in during the period 2010-2013, do not have a publishing option compliant with the Wellcome Trust open access policy. Data released under CC0 Public Domain Mark <br><br>
DOI: 10.6084/m9.figshare.1152693
title: Liraglutide consolidated list of published & unpublished studies

description: Liraglutide list of unpublished studies Ramirez, Jorge H (2014): Analysis of published and unpublished liraglutide studies in humans. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.1134664 Retrieved 14:03, Aug 27, 2014 (GMT)
DOI: 10.6084/m9.figshare.1152725.v2
title: Independent data set of occurrence points T. infestans and R. prolixus

description: Independent data set of occurence points of <em>R. prolixus</em> from Venezuela, and <em>T. infestans</em> from Argentina species.
DOI: 10.6084/m9.figshare.1152725.v3
title: Independent data set of occurrence points T. infestans and R. prolixus

description: Independent data set of occurence points of <em>R. prolixus</em> from Venezuela, and <em>T. infestans</em> from Argentina species.
DOI: 10.6084/m9.figshare.1152727.v2
title: Marine microbial eukaryote transcriptomes

description: Assemblies of publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes.
DOI: 10.6084/m9.figshare.1152727.v3
title: Marine microbial eukaryote transcriptomes

description: Assemblies of publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes.
DOI: 10.6084/m9.figshare.1152688
title: Measuring and Visualizing Energy Consumption within Software Code

description: Poster presented at the VL/HCC'14 Graduate Consorcium by Tiago Carção
DOI: 10.6084/m9.figshare.1152693.v1
title: Liraglutide list of unpublished studies

description: Liraglutide list of unpublished studies Ramirez, Jorge H (2014): Analysis of published and unpublished liraglutide studies in humans. figshare.<br>http://dx.doi.org/10.6084/m9.figshare.1134664Retrieved 14:03, Aug 27, 2014 (GMT)
DOI: 10.6084/m9.figshare.1152691.v1
title: List of journals that do not provide a publishing option compliant with the Trust's OA policy

description: Using Sherpa FACT (http://www.sherpa.ac.uk/fact/) and our own repository of publisher correspondence, we undertook an analysis to determine which of the journals Wellcome Trust authors published in during the period 2010-2013, do not have a publishing option compliant with the Wellcome Trust open access policy. <br><br>
DOI: 10.6084/m9.figshare.1152727.v4
title: Marine microbial eukaryote transcriptomes

description: Assemblies of publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes.
DOI: 10.6084/m9.figshare.1152727.v5
title: Marine microbial eukaryote transcriptomes

description: Assemblies of publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes.
DOI: 10.6084/m9.figshare.1152727.v6
title: Marine microbial eukaryote transcriptomes

description: Assemblies of publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes.
DOI: 10.6084/m9.figshare.1152727.v7
title: Marine microbial eukaryote transcriptomes

description: <strong>Overview</strong> This repository provides assemblies of publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes. The raw data were generated by the Marine Microbial Eukaryote Transcriptome Sequencing Project (http://marinemicroeukaryotes.org/). This project provides its own set of assemblies (generated using the Abyss assembler). Since our work-flows are geared towards assemblies generated by the Trinity assembler, raw data were obtained from the following website http://marinemicroeukaryotes.org/ and assembled using Trinity (http://trinityrnaseq.sourceforge.net/) For our purposes the raw data were directly assembled using Trinity (see README for version number) using the default settings. Several species/strains were assembled using all available Illumina libraries combined (see README). The identifiers of the raw data are provided and culture conditions of the organisms can be retrieved from http://marinemicroeukaryotes.org/ using the MMETSP ID (see README for list). <strong>If you use these data please cite</strong> Keeling, P.J. et al., 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLoS Biology, 12:e1001889. Grabherr, M.G. et al., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29:644-652. <strong>Funding</strong> NSF Dimensions of Biodiversity Grant DEB-1046075
DOI: 10.6084/m9.figshare.1152727.v8
title: Marine microbial eukaryote transcriptomes

description: <strong>Overview</strong> This repository provides assemblies of publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes. The raw data were generated by the Marine Microbial Eukaryote Transcriptome Sequencing Project (http://marinemicroeukaryotes.org/). This project provides its own set of assemblies (generated using the Abyss assembler). Since our work-flows are geared towards assemblies generated by the Trinity assembler, raw data were obtained from the following website http://marinemicroeukaryotes.org/ and assembled using Trinity (http://trinityrnaseq.sourceforge.net/) For our purposes the raw data were directly assembled using Trinity (see README for version number) using the default settings. Several species/strains were assembled using all available Illumina libraries combined (see README). The identifiers of the raw data are provided and culture conditions of the organisms can be retrieved from http://marinemicroeukaryotes.org/ using the MMETSP ID (see README for list). <strong>If you use these data please cite</strong> Keeling, P.J. et al., 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLoS Biology, 12:e1001889. Grabherr, M.G. et al., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29:644-652. <strong>Funding</strong> NSF Dimensions of Biodiversity Grant DEB-1046075
DOI: 10.6084/m9.figshare.1151596
title: Scaled Quantum Chemical Studies of the Molecular Structure and Vibrational Spectra of Minoxidil

description: The Fourier transform Raman and Fourier transform infrared spectra for minoxidil have been recorded in the region 4000—100 cm<sup>−1</sup> and 4000—450 cm<sup>−1</sup>, respectively. The structural and spectroscopy data of the molecule in the ground state were calculated by using density functional theory methods with 6-311G (d, p) basis set. A detailed vibrational analysis of the title compound has been done using normal coordinate analysis following the scaled quantum mechanical force field methodology. The calculated molecular geometry parameters and scaled vibrational wavenumbers are well compared with the experimental data. The electronic properties, such as excitation energies, absorption wavelength, highest occupied molecular orbital (HOMO), and lowest unoccupied molecular orbital (LUMO) energies were performed by time-dependent density functional theory approach, and the results are in good agreement with experimental absorption spectrum. The charge delocalizations of these molecules have been analyzed using natural bond orbital analysis. The molecule orbital contributions are studied by density of energy states. Fukui functions, local softness, and electrophilicity indices for selected atomic sites of the title compound are determined. Finally, the thermal behaviors of the compound have been calculated by different temperature.
DOI: 10.6084/m9.figshare.1151596.v1
title: Scaled Quantum Chemical Studies of the Molecular Structure and Vibrational Spectra of Minoxidil

description: The Fourier transform Raman and Fourier transform infrared spectra for minoxidil have been recorded in the region 4000—100 cm<sup>−1</sup> and 4000—450 cm<sup>−1</sup>, respectively. The structural and spectroscopy data of the molecule in the ground state were calculated by using density functional theory methods with 6-311G (d, p) basis set. A detailed vibrational analysis of the title compound has been done using normal coordinate analysis following the scaled quantum mechanical force field methodology. The calculated molecular geometry parameters and scaled vibrational wavenumbers are well compared with the experimental data. The electronic properties, such as excitation energies, absorption wavelength, highest occupied molecular orbital (HOMO), and lowest unoccupied molecular orbital (LUMO) energies were performed by time-dependent density functional theory approach, and the results are in good agreement with experimental absorption spectrum. The charge delocalizations of these molecules have been analyzed using natural bond orbital analysis. The molecule orbital contributions are studied by density of energy states. Fukui functions, local softness, and electrophilicity indices for selected atomic sites of the title compound are determined. Finally, the thermal behaviors of the compound have been calculated by different temperature.
DOI: 10.6084/m9.figshare.1151572
title: Comparison of the monomer structure of the FMN-binding protein from <i>Desulfovibrio vulgaris</i> obtained by NMR and molecular dynamics simulation approaches

description: Flavin mononucleotide (FMN)-binding proteins (FBPs) play an important role in the electron transport process in bacteria. In this study, the structures of the FBP from <i>Desulfovibrio vulgaris</i> (<i>Dv</i>FBP) (Miyazaki F) were compared between those obtained experimentally by nuclear magnetic resonance (NMR) spectroscopy and those derived from molecular dynamics simulations (MDSs). A high-residue root of mean square deviation (RMSD) was observed in residues located at both sides of the wings (Gly22, Glu23, Asp24, Ala59, Arg60, Asp61, Glu62, Gly75, Arg76, Asn77, Gly78 and Pro79), while a low-residue RMSD was found in residues located in a hollow of the structure (Asn12, Glu13, Gly14, Val15, Val16, Asn30, Thr31, Trp32, Asn33, Ser34, Gly69, Ser70, Arg71 and Lys72). Inter-planar angles between the Phe7 and Iso and between the Phe7 and Trp106 residues were remarkably different between the MDS- and NMR-derived <i>Dv</i>FBP structures. Distribution of the torsion angles around the covalent bonds in the aliphatic chain of FMN was similar in the MDS- and NMR-derived structures, except for those around the C1′–C2′ and C5′–O5′ bonds. Hydrogen bond formation between IsoO2 and the Gly49 or Gly50 peptide NH was formed in both the NMR- and MDS-derived structures. Overall, the MDS-derived structures were found to be considerably different from the NMR-derived structures, which must be considered when the photoinduced electron transfer in flavoproteins is analysed with MDS-derived structures.
DOI: 10.6084/m9.figshare.1151572.v1
title: Comparison of the monomer structure of the FMN-binding protein from <i>Desulfovibrio vulgaris</i> obtained by NMR and molecular dynamics simulation approaches

description: Flavin mononucleotide (FMN)-binding proteins (FBPs) play an important role in the electron transport process in bacteria. In this study, the structures of the FBP from <i>Desulfovibrio vulgaris</i> (<i>Dv</i>FBP) (Miyazaki F) were compared between those obtained experimentally by nuclear magnetic resonance (NMR) spectroscopy and those derived from molecular dynamics simulations (MDSs). A high-residue root of mean square deviation (RMSD) was observed in residues located at both sides of the wings (Gly22, Glu23, Asp24, Ala59, Arg60, Asp61, Glu62, Gly75, Arg76, Asn77, Gly78 and Pro79), while a low-residue RMSD was found in residues located in a hollow of the structure (Asn12, Glu13, Gly14, Val15, Val16, Asn30, Thr31, Trp32, Asn33, Ser34, Gly69, Ser70, Arg71 and Lys72). Inter-planar angles between the Phe7 and Iso and between the Phe7 and Trp106 residues were remarkably different between the MDS- and NMR-derived <i>Dv</i>FBP structures. Distribution of the torsion angles around the covalent bonds in the aliphatic chain of FMN was similar in the MDS- and NMR-derived structures, except for those around the C1′–C2′ and C5′–O5′ bonds. Hydrogen bond formation between IsoO2 and the Gly49 or Gly50 peptide NH was formed in both the NMR- and MDS-derived structures. Overall, the MDS-derived structures were found to be considerably different from the NMR-derived structures, which must be considered when the photoinduced electron transfer in flavoproteins is analysed with MDS-derived structures.
DOI: 10.6084/m9.figshare.1151546
title: Queen's University Belfast RCUK Call for Evidence Data 2013-14

description: This dataset provides a list of known articles, authored by Queen's University Belfast researchers, that are outcomes of RCUK funded projects. The set provides information on any article processing charges (APCs) that were paid by Queen's University Belfast from the RCUK Block Grant for Open Access as well as the open access and licence status for all known articles. This dataset is not necessarily a comprehensive list of all RCUK funded research outputs authored by Queen's researchers, it only includes articles where RCUK has been acknowledged and are discoverable in Web of Science or those that have been made open access via the RCUK Open Access Block Grant.
DOI: 10.6084/m9.figshare.1151544
title: Fig f7 - PCA_ATGL_Lipidome

description: PCA scatter plot for the whole lipid droplet lipidome demonstrating clear separation of the 4 sample groups in the ATGL-study.
DOI: 10.6084/m9.figshare.1151544.v1
title: Fig f7 - PCA_ATGL_Lipidome

description: PCA scatter plot for the whole lipid droplet lipidome demonstrating clear separation of the 4 sample groups in the ATGL-study.
DOI: 10.6084/m9.figshare.1151543
title: Unearthing earthquakes and their tsunamis using multiple proxies: the 22 June 1932 event and a probable fourteenth-century predecessor on the Pacific coast of Mexico

description: Tsunami deposits have been widely studied in temperate latitudes, but the intrinsic difficulties associated with tropical coastal environments, and the intensity of bioturbation in these habitats, limit the possibilities of analysing these formations. Here, we investigate the deposits on the Colima coast of Mexico, which overlies the subducting Rivera and Cocos Plates, in order to reconstruct the tsunami inundation history and related hazard. We developed a multi-proxy study aimed to recognize and date historical and palaeotsunami deposits, including historical data on the effects of a known tsunami, geomorphological mapping, stratigraphic, grain size, organic matter content, diatoms, geochemical composition, magnetic susceptibility, and anisotropy of magnetic susceptibility, together with radiometric dating (<sup>210</sup>Pb and <sup>14</sup>C). We identified two probable tsunami deposits at Palo Verde estuary including a historical event associated with the Mw 6.9 earthquake on 22 June 1932 and a palaeotsunami most likely generated by a similar event in the fourteenth century. This work shows that it is possible to identify both historical and palaeotsunamis in the tropical environment of Mexico’s Pacific coast. These data will serve to enhance our understanding of tsunami deposits in tropical environments and of the regional tsunami hazard.
DOI: 10.6084/m9.figshare.1151546.v4
title: Queen's University Belfast RCUK Call for Evidence Data 2013-14

description: This dataset provides a list of known articles, authored by Queen's University Belfast researchers, that are outcomes of RCUK funded projects. The set provides information on any article processing charges (APCs) that were paid by Queen's University Belfast from the RCUK Block Grant for Open Access as well as the open access and licence status for all known articles. This dataset is not necessarily a comprehensive list of all RCUK funded research outputs authored by Queen's researchers, it only includes articles where RCUK has been acknowledged and are discoverable in Web of Science or those that have been made open access via the RCUK Open Access Block Grant.
DOI: 10.6084/m9.figshare.1151542
title: Results Beta-glucan trial

description: Results Beta-glucan trial
DOI: 10.6084/m9.figshare.1151541
title: The differential diffusion effect of the intermediate species on the stability of premixed flames propagating in microchannels

description: The propagation of premixed flames in adiabatic and non-catalytic planar microchannels subject to an assisted or opposed Poiseuille flow is considered. The diffusive–thermal model and the well-known two-step chain-branching kinetics are used in order to investigate the role of the differential diffusion of the intermediate species on the spatial and temporal flame stability. This numerical study successfully compares steady-state and time-dependent computations to the linear stability analysis of the problem. Results show that for fuel Lewis numbers less than unity, <i>Le</i><sub><i>F</i></sub> &lt; 1, and at sufficiently large values of the opposed Poiseuille flow rate, symmetry-breaking bifurcation arises. It is seen that small values of the radical Lewis number, <i>Le</i><sub><i>Z</i></sub>, stabilise the flame to symmetric shape solutions, but result in earlier flashback. For very lean flames, the effect of the radical on the flame stabilisation becomes less important due to the small radical concentration typically found in the reaction zone. Cellular flame structures were also identified in this regime. For <i>Le</i><sub><i>F</i></sub> &gt; 1, flames propagating in adiabatic channels suffer from oscillatory instabilities. The Poiseuille flow stabilises the flame and the effect of <i>Le</i><sub><i>Z</i></sub> is opposite to that found for <i>Le</i><sub><i>F</i></sub> &lt; 1. Small values of <i>Le</i><sub><i>Z</i></sub> further destabilise the flame to oscillating or pulsating instabilities.
DOI: 10.6084/m9.figshare.1151546.v3
title: RCUK Call for Evidence Data 2013-14

description: This dataset provides a list of known articles, authored by Queen's University Belfast researchers, that are outcomes of RCUK funded projects. The set provides information on any article processing charges (APCs) that were paid by Queen's University Belfast from the RCUK Block Grant for Open Access as well as the open access and licence status for all known articles. This dataset is not necessarily a comprehensive list of all RCUK funded research outputs authored by Queen's researchers, it only includes articles where RCUK has been acknowledged and are discoverable in Web of Science or those that have been made open access via the RCUK Open Access Block Grant.
DOI: 10.6084/m9.figshare.1151541.v2
title: The differential diffusion effect of the intermediate species on the stability of premixed flames propagating in microchannels

description: The propagation of premixed flames in adiabatic and non-catalytic planar microchannels subject to an assisted or opposed Poiseuille flow is considered. The diffusive–thermal model and the well-known two-step chain-branching kinetics are used in order to investigate the role of the differential diffusion of the intermediate species on the spatial and temporal flame stability. This numerical study successfully compares steady-state and time-dependent computations to the linear stability analysis of the problem. Results show that for fuel Lewis numbers less than unity, <i>Le</i><sub><i>F</i></sub> &lt; 1, and at sufficiently large values of the opposed Poiseuille flow rate, symmetry-breaking bifurcation arises. It is seen that small values of the radical Lewis number, <i>Le</i><sub><i>Z</i></sub>, stabilise the flame to symmetric shape solutions, but result in earlier flashback. For very lean flames, the effect of the radical on the flame stabilisation becomes less important due to the small radical concentration typically found in the reaction zone. Cellular flame structures were also identified in this regime. For <i>Le</i><sub><i>F</i></sub> &gt; 1, flames propagating in adiabatic channels suffer from oscillatory instabilities. The Poiseuille flow stabilises the flame and the effect of <i>Le</i><sub><i>Z</i></sub> is opposite to that found for <i>Le</i><sub><i>F</i></sub> &lt; 1. Small values of <i>Le</i><sub><i>Z</i></sub> further destabilise the flame to oscillating or pulsating instabilities.