cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1404123
title: Cylindrical Wave Field Experiments - Photos

description: This fileset contains photos of the experiments. Experiments were conducted in the University of Edinburgh Curved Wave Tank to determine the linear cylindrical coefficients for progressive water waves. The experiments employed two body geometries, an attenuator consisting of a horizontal pitching cylinder, and a terminator made up of a bottom-hinged flap. An array of 59 wave gauges was arranged in a circle-spoke pattern, where the circle of wave gauges was necessary for deriving the cylindrical coefficients, and the spokes, which extended radially further afield, were used for validation. Both the scattered and the radiated waves of the bodies were examined at three frequencies.
DOI: 10.6084/m9.figshare.1404120
title: Cylindrical Wave Field Experiments - Body

description: This file set contains information about the geometries/models used in the experiments. Experiments were conducted in the University of Edinburgh Curved Wave Tank to determine the linear cylindrical coefficients for progressive water waves. The experiments employed two body geometries, an attenuator consisting of a horizontal pitching cylinder, and a terminator made up of a bottom-hinged flap. An array of 59 wave gauges was arranged in a circle-spoke pattern, where the circle of wave gauges was necessary for deriving the cylindrical coefficients, and the spokes, which extended radially further afield, were used for validation. Both the scattered and the radiated waves of the bodies were examined at three frequencies.
DOI: 10.6084/m9.figshare.1404121.v1
title: Cylindrical Wave Field Experiments - Wave

description: This fileset contains information about the incident waves, including the input files to the wave maker software. Experiments were conducted in the University of Edinburgh Curved Wave Tank to determine the linear cylindrical coefficients for progressive water waves. The experiments employed two body geometries, an attenuator consisting of a horizontal pitching cylinder, and a terminator made up of a bottom-hinged flap. An array of 59 wave gauges was arranged in a circle-spoke pattern, where the circle of wave gauges was necessary for deriving the cylindrical coefficients, and the spokes, which extended radially further afield, were used for validation. Both the scattered and the radiated waves of the bodies were examined at three frequencies.
DOI: 10.6084/m9.figshare.1404123.v1
title: Cylindrical Wave Field Experiments - Photos

description: This fileset contains photos of the experiments. Experiments were conducted in the University of Edinburgh Curved Wave Tank to determine the linear cylindrical coefficients for progressive water waves. The experiments employed two body geometries, an attenuator consisting of a horizontal pitching cylinder, and a terminator made up of a bottom-hinged flap. An array of 59 wave gauges was arranged in a circle-spoke pattern, where the circle of wave gauges was necessary for deriving the cylindrical coefficients, and the spokes, which extended radially further afield, were used for validation. Both the scattered and the radiated waves of the bodies were examined at three frequencies.
DOI: 10.6084/m9.figshare.1404118
title: Molecular docking and dynamics simulations on the interaction of cationic porphyrin–anthraquinone hybrids with DNA G-quadruplexes

description: A series of cationic porphyrin–anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the <i>meso</i>-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction.
DOI: 10.6084/m9.figshare.1403711
title: The Power and Potential of Automating Care

description: The incorporation of computers into clinical settings has led to the rise in the use of the term "automation" as a buzzword. However, the status of this term as a buzzword vastly overestimates the role automation plays versus what it could play in the clinical context. Despite vast opportunities offered by the expansion of automation into care systems, major gaps remain in the infrastructure required to support its widespread introduction. Fortunately, tools like RexDB by Prometheus Research can facilitate such an infrastructure.
DOI: 10.6084/m9.figshare.1404120.v3
title: Cylindrical Wave Field Experiments - Body

description: This file set contains information about the geometries/models used in the experiments. Experiments were conducted in the University of Edinburgh Curved Wave Tank to determine the linear cylindrical coefficients for progressive water waves. The experiments employed two body geometries, an attenuator consisting of a horizontal pitching cylinder, and a terminator made up of a bottom-hinged flap. An array of 59 wave gauges was arranged in a circle-spoke pattern, where the circle of wave gauges was necessary for deriving the cylindrical coefficients, and the spokes, which extended radially further afield, were used for validation. Both the scattered and the radiated waves of the bodies were examined at three frequencies.
DOI: 10.6084/m9.figshare.1404118.v1
title: Molecular docking and dynamics simulations on the interaction of cationic porphyrin–anthraquinone hybrids with DNA G-quadruplexes

description: A series of cationic porphyrin–anthraquinone hybrids bearing either pyridine, imidazole, or pyrazole rings at the <i>meso</i>-positions have been investigated for their interaction with DNA G-quadruplexes by employing molecular docking and molecular dynamics simulations. Three types of DNA G-quadruplexes were utilized, which comprise parallel, antiparallel, and mixed hybrid topologies. The porphyrin hybrids have a preference to bind with parallel and mixed hybrid structures compared to the antiparallel structure. This preference arises from the end stacking of porphyrin moiety following G-stem and loop binding of anthraquinone tail, which is not found in the antiparallel due to the presence of diagonal and lateral loops that crowd the G-quartet. The binding to the antiparallel, instead, occurred with poorer affinity through both the loop and wide groove. All sites of porphyrin binding were confirmed by 6 ns molecular dynamics simulation, as well as by the negative value of the total binding free energies that were calculated using the MMPBSA method. Free energy analysis shows that the favorable contribution came from the electrostatic term, which supposedly originated from the interaction of either cationic pyridinium, pyrazole, or imidazole groups and the anionic phosphate backbone, and also from the van der Waals energy, which primarily contributed through end stacking interaction.
DOI: 10.6084/m9.figshare.1404120.v2
title: Cylindrical Wave Field Experiments - Body

description: This file set contains information about the geometries/models used in the experiments. Experiments were conducted in the University of Edinburgh Curved Wave Tank to determine the linear cylindrical coefficients for progressive water waves. The experiments employed two body geometries, an attenuator consisting of a horizontal pitching cylinder, and a terminator made up of a bottom-hinged flap. An array of 59 wave gauges was arranged in a circle-spoke pattern, where the circle of wave gauges was necessary for deriving the cylindrical coefficients, and the spokes, which extended radially further afield, were used for validation. Both the scattered and the radiated waves of the bodies were examined at three frequencies.
DOI: 10.6084/m9.figshare.1403711.v2
title: The Power and Potential of Automating Care

description: The incorporation of computers into clinical settings has led to the rise in the use of the term "automation" as a buzzword. However, the status of this term as a buzzword vastly overestimates the role automation plays versus what it could play in the clinical context. Despite vast opportunities offered by the expansion of automation into care systems, major gaps remain in the infrastructure required to support its widespread introduction. Fortunately, tools like RexDB by Prometheus Research can facilitate such an infrastructure.
DOI: 10.6084/m9.figshare.1403711.v1
title: The Power and Potential of Automating Care

description: The incorporation of computers into clinical settings has led to the rise in the use of the term "automation" as a buzzword. However, the status of this term as a buzzword vastly overestimates the role automation plays versus what it could play in the clinical context. Despite vast opportunities offered by the expansion of automation into care systems, major gaps remain in the infrastructure required to support its widespread introduction. Fortunately, tools like RexDB by Prometheus Research can facilitate such an infrastructure.
DOI: 10.6084/m9.figshare.1409398.v165
title: ABO phenotype protected reproduction as it is based on fucosylations

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation of the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1403630
title: Trait-based metrics in the deep sea

description: Supporting data for the paper: Mindel, B.L., Webb, T.J., Neat, F.C. & Blanchard, J.L. (2016) A trait-based metric sheds new light on the nature of the body size–depth relationship in the deep sea. <i>Journal of Animal Ecology</i>, 85, 427-436.Datasets have been summarised to enable replication of figures and analyses from this paper. Data are provided by Marine Scotland Science from their ongoing deepwater trawl survey. See links for individual datasets and their descriptions.
DOI: 10.6084/m9.figshare.1403628
title: RDA - species composition

description: Redundancy Analysis of the effect of depth on the biomass of species in stations. Depth of stations is also required as an input and can be found in 'Values per station'. Species names can be found in 'Species codes'. See link for fileset description.
DOI: 10.6084/m9.figshare.1403629
title: RDA - body size

description: Redundancy Analysis of the effect of depth on the body size of species in stations. Depth of stations is also required as an input and can be found in 'Values per station'. Species names can be found in 'Species codes'. See link for fileset description.
DOI: 10.6084/m9.figshare.1409398.v166
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation of the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1403630.v1
title: Trait-based metrics in the deep sea

description: Supporting data for the paper: Mindel, B.L., Webb, T.J., Neat, F.C. & Blanchard, J.L. (2016) A trait-based metric sheds new light on the nature of the body size–depth relationship in the deep sea. <i>Journal of Animal Ecology</i>, 85, 427-436.Datasets have been summarised to enable replication of figures and analyses from this paper. Data are provided by Marine Scotland Science from their ongoing deepwater trawl survey. See links for individual datasets and their descriptions.
DOI: 10.6084/m9.figshare.1403628.v1
title: RDA - species composition

description: Redundancy Analysis of the effect of depth on the biomass of species in stations. Depth of stations is also required as an input and can be found in 'Values per station'. Species names can be found in 'Species codes'. See link for fileset description.
DOI: 10.6084/m9.figshare.1403626
title: Species codes

description: The translation of the codes used on the survey and in the datasets to full Latin species names. See link for fileset description.
DOI: 10.6084/m9.figshare.1403627
title: Values per station

description: Mean depth of stations along with values of the metrics per station, i.e. across species (c.f. datasets labelled as 'RDA' which contain values for each species). These values produce panel b) of figures 2, 3 and 4 in the paper, and the associated LM/GAM. See link for fileset description.
DOI: 10.6084/m9.figshare.1403629.v1
title: RDA - body size

description: Redundancy Analysis of the effect of depth on the body size of species in stations. Depth of stations is also required as an input and can be found in 'Values per station'. Species names can be found in 'Species codes'. See link for fileset description.
DOI: 10.6084/m9.figshare.1403624
title: Intra- and inter-specific body size analysis

description: The data to produce the discussed relationships between body size and depth for individual species. The slope, standard error, p value, positive/negative, and significant/non-significant columns come from the relationship between body length and depth for individuals of the listed species. Maximum size and maximum depth come from all data on the survey. See link for fileset description.
DOI: 10.6084/m9.figshare.1403625
title: RDA - fractional size

description: Redundancy Analysis of the effect of depth on the fractional size (length/maximum length) of species in stations. Depth of stations is also required as an input and can be found in 'Values per station'. Species names can be found in 'Species codes'. See link for fileset description.
DOI: 10.6084/m9.figshare.1403627.v1
title: Values per station

description: Mean depth of stations along with values of the metrics per station, i.e. across species (c.f. datasets labelled as 'RDA' which contain values for each species). These values produce panel b) of figures 2, 3 and 4 in the paper, and the associated LM/GAM. See link for fileset description.
DOI: 10.6084/m9.figshare.1409398.v167
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation of the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leucospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, the non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins that might promote increased anti-self-reactive cytotoxicity.
DOI: 10.6084/m9.figshare.1403626.v1
title: Species codes

description: The translation of the codes used on the survey and in the datasets to full Latin species names. See link for fileset description.
DOI: 10.6084/m9.figshare.1403622
title: Figure 3a - size of species

description: Data to produce figure 3a - size of species in 100m depth bands. Species names can be found in 'Species codes'. See link for fileset description.
DOI: 10.6084/m9.figshare.1403623
title: Figure 4a - species biomass

description: Data to produce figure 4a - biomass per hour of species in 100m depth bands. Species names can be found in 'Species codes'. See link for fileset description.
DOI: 10.6084/m9.figshare.1403624.v1
title: Intra- and inter-specific body size analysis

description: The data to produce the discussed relationships between body size and depth for individual species. The slope, standard error, p value, positive/negative, and significant/non-significant columns come from the relationship between body length and depth for individuals of the listed species. Maximum size and maximum depth come from all data on the survey. See link for fileset description.
DOI: 10.6084/m9.figshare.1403625.v1
title: RDA - fractional size

description: Redundancy Analysis of the effect of depth on the fractional size (length/maximum length) of species in stations. Depth of stations is also required as an input and can be found in 'Values per station'. Species names can be found in 'Species codes'. See link for fileset description.
DOI: 10.6084/m9.figshare.1403623.v1
title: Figure 4a - species biomass

description: Data to produce figure 4a - biomass per hour of species in 100m depth bands. Species names can be found in 'Species codes'. See link for fileset description.
DOI: 10.6084/m9.figshare.1403617
title: University of Sheffield APCs 2015 (Jan-July)

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Sheffield during the first half of 2015 (1 January - 18 July). The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/) and has been released with permission of the University of Sheffield Library. Updated on 31 July to include figures up to an including 18 July.
DOI: 10.6084/m9.figshare.1403621
title: Figure 2a - fractional size of species

description: Data to produce figure 2a - fractional size (length/maximum length) of species in 100m depth bands. Species names can be found in 'Species codes'. See link for fileset description.