cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4601968.v1
title: Table S3. Uranium–lead zircon systematics in the Sudbury impact crater-fill: implications for target lithologies and crater evolution

description: Table S3: Isotopic modelling parameters
DOI: 10.6084/m9.figshare.4601941
title: A novel mycobacterial in vitro infection assay identifies differences of induced macrophage apoptosis between CD4+ and CD8+ T cells

description: Deduced proportions of immune cells and phenotypic markers<br>
DOI: 10.6084/m9.figshare.4601935
title: Removal of copper from aqueous solutions by rhizofiltration using genetically modified hairy roots expressing a bacterial Cu-binding protein

description: The aim of this work was to develop a biotechnological tool to hyperaccumulate high copper (Cu) concentrations from wastewaters. Transgenic tobacco hairy roots were obtained by expressing, either the wild-type version of the gene <i>copC</i> from <i>Pseudomonas fluorescens</i> in the cytoplasm of plant cells (CuHR), or a modified version targeted to the vacuole (CuHR-V). Control hairy roots transformed with the empty vector (HR) were also generated. The roots were incubated in the presence of solutions containing Cu (from 1 to 50 mM). At 5 mM external copper, transgenic hairy roots accumulated twice the amount of copper accumulated by control hairy roots. However, at 50 mM Cu, accumulation in both transgenic and control roots reached similar values. Maximum Cu accumulation achieved by transgenic hairy roots was 45,000 µg g<sup>−1</sup> at 50 mM external Cu. Despite the high Cu accumulation, transgenic hairy roots, particularly CuHR-V, showed less toxicity symptoms, in correlation with lower activity of several antioxidant enzymes and lower malondialdehyde (MDA) levels. Moreover, CuHR-V roots displayed low values of the oxidative stress index (OSI) – a global parameter proposed for oxidative stress – indicating that targeting CopC to the vacuole could alleviate the oxidative stress caused by Cu. Our results suggest that expressing <i>copC</i> in transgenic hairy roots is a suitable strategy to obtain Cu-hyperaccumulator hairy roots with less toxicity stress symptoms. <b>Abbreviations</b>: APX: ascorbate peroxidase; ATSDR: Agency for Toxic Substances and Disease Registry (U.S.); BCF: bioconcentration factor; CuHR: <i>copper-hairy roots</i>; EDTA: ethylenediamine tetracetic acid; EPA: Environmental Protection Agency (U.S.); GSH: glutathione; HM: heavy metals; HR: control hairy roots; ICP-OES: Inductively Coupled Plasma/Optical Emission Spectrometry; MDA: malondialdehyde; NBT: nitroblue tetrazolium; OD: optical density; OSI: oxidative stress index; PCR: polymerase chain reaction; PVP: polyvynilpirrolidone; PX: peroxidase; ROS: reactive oxygen species; SOD: superoxide dismutase
DOI: 10.6084/m9.figshare.4601938
title: Chef-Brain-PlosOne2017

description: Here you can find neuroimaging data about the paper: Cerasa et al. <i>Increased cerebellar gray matter volume in head Chefs</i>. Plos One 2017; DOI: 10.1371/journal.pone.0171457
DOI: 10.6084/m9.figshare.4601941.v1
title: A novel mycobacterial in vitro infection assay identifies differences of induced macrophage apoptosis between CD4+ and CD8+ T cells

description: Deduced proportions of immune cells and phenotypic markers<br>
DOI: 10.6084/m9.figshare.4601935.v1
title: Removal of copper from aqueous solutions by rhizofiltration using genetically modified hairy roots expressing a bacterial Cu-binding protein

description: The aim of this work was to develop a biotechnological tool to hyperaccumulate high copper (Cu) concentrations from wastewaters. Transgenic tobacco hairy roots were obtained by expressing, either the wild-type version of the gene <i>copC</i> from <i>Pseudomonas fluorescens</i> in the cytoplasm of plant cells (CuHR), or a modified version targeted to the vacuole (CuHR-V). Control hairy roots transformed with the empty vector (HR) were also generated. The roots were incubated in the presence of solutions containing Cu (from 1 to 50 mM). At 5 mM external copper, transgenic hairy roots accumulated twice the amount of copper accumulated by control hairy roots. However, at 50 mM Cu, accumulation in both transgenic and control roots reached similar values. Maximum Cu accumulation achieved by transgenic hairy roots was 45,000 µg g<sup>−1</sup> at 50 mM external Cu. Despite the high Cu accumulation, transgenic hairy roots, particularly CuHR-V, showed less toxicity symptoms, in correlation with lower activity of several antioxidant enzymes and lower malondialdehyde (MDA) levels. Moreover, CuHR-V roots displayed low values of the oxidative stress index (OSI) – a global parameter proposed for oxidative stress – indicating that targeting CopC to the vacuole could alleviate the oxidative stress caused by Cu. Our results suggest that expressing <i>copC</i> in transgenic hairy roots is a suitable strategy to obtain Cu-hyperaccumulator hairy roots with less toxicity stress symptoms. <b>Abbreviations</b>: APX: ascorbate peroxidase; ATSDR: Agency for Toxic Substances and Disease Registry (U.S.); BCF: bioconcentration factor; CuHR: <i>copper-hairy roots</i>; EDTA: ethylenediamine tetracetic acid; EPA: Environmental Protection Agency (U.S.); GSH: glutathione; HM: heavy metals; HR: control hairy roots; ICP-OES: Inductively Coupled Plasma/Optical Emission Spectrometry; MDA: malondialdehyde; NBT: nitroblue tetrazolium; OD: optical density; OSI: oxidative stress index; PCR: polymerase chain reaction; PVP: polyvynilpirrolidone; PX: peroxidase; ROS: reactive oxygen species; SOD: superoxide dismutase
DOI: 10.6084/m9.figshare.4601938.v1
title: Chef-Brain-PlosOne2017

description: Here you can find neuroimaging data about the paper: Cerasa et al. <i>Increased cerebellar gray matter volume in head Chefs</i>. Plos One 2017; DOI: 10.1371/journal.pone.0171457
DOI: 10.6084/m9.figshare.4601905
title: Data for table 1 and figure 3-10 from Evaluation of natural sounds in urban greenery: potential impact for urban nature preservation

description: Most humans now live in cities and their main experience of nature is through urban greenery. An increasing number of studies show the importance of urban green spaces for well-being, although most of them are based on visual perception. A questionnaire examining people's evaluations of natural sounds was answered by 1326 individuals living near one of six urban green areas of varying naturalness in the city of Gothenburg, Sweden. Women and the elderly reported greater calmness when hearing bird song and rustling leaves (and placed a higher importance on the richness of bird species) than did men, younger and middle-aged individuals. Independent of age and gender, urban woodlands (high naturalness) had higher evaluations than parks (low naturalness). Our results suggest that to increase positive experiences of urban green areas, demographic variables of gender and age should be taken into account, and settings that mimic nature should be prioritized in planning.
DOI: 10.6084/m9.figshare.4601905.v1
title: Data for table 1 and figure 3-10 from Evaluation of natural sounds in urban greenery: potential impact for urban nature preservation

description: Most humans now live in cities and their main experience of nature is through urban greenery. An increasing number of studies show the importance of urban green spaces for well-being, although most of them are based on visual perception. A questionnaire examining people's evaluations of natural sounds was answered by 1326 individuals living near one of six urban green areas of varying naturalness in the city of Gothenburg, Sweden. Women and the elderly reported greater calmness when hearing bird song and rustling leaves (and placed a higher importance on the richness of bird species) than did men, younger and middle-aged individuals. Independent of age and gender, urban woodlands (high naturalness) had higher evaluations than parks (low naturalness). Our results suggest that to increase positive experiences of urban green areas, demographic variables of gender and age should be taken into account, and settings that mimic nature should be prioritized in planning.
DOI: 10.6084/m9.figshare.4601938.v2
title: Chef-Brain-PlosOne2017

description: Here you can find neuroimaging data about the paper: Cerasa et al. <i>Increased cerebellar gray matter volume in head Chefs</i>. Plos One 2017; DOI: 10.1371/journal.pone.0171457
DOI: 10.6084/m9.figshare.4601938.v3
title: Chef-Brain-PlosOne2017

description: Here you can find neuroimaging data about the paper: Cerasa et al. <i>Increased cerebellar gray matter volume in head Chefs</i>. Plos One 2017; DOI: 10.1371/journal.pone.0171457
DOI: 10.6084/m9.figshare.4601938.v4
title: Chef-Brain-PlosOne2017

description: Here you can find neuroimaging data about the paper: Cerasa et al. <i>Increased cerebellar gray matter volume in head Chefs</i>. Plos One 2017; DOI: 10.1371/journal.pone.0171457
DOI: 10.6084/m9.figshare.4601938.v6
title: Chef-Brain-PlosOne2017

description: Here you can find neuroimaging data about the paper: Cerasa et al. <i>Increased cerebellar gray matter volume in head Chefs</i>. Plos One 2017; DOI: 10.1371/journal.pone.0171457
DOI: 10.6084/m9.figshare.4601938.v5
title: Chef-Brain-PlosOne2017

description: Here you can find neuroimaging data about the paper: Cerasa et al. <i>Increased cerebellar gray matter volume in head Chefs</i>. Plos One 2017; DOI: 10.1371/journal.pone.0171457
DOI: 10.6084/m9.figshare.4600420
title: Hungate_qSIP_metadata.xlsx

description: This excel file contains metadata associated with MG-RAST project hungate_qSIP (mgp14151). It contains data on gene abundance (16S rRNA via quantitative PCR), fraction density, fraction DNA concentration, and other descriptive information.
DOI: 10.6084/m9.figshare.4600645
title: Supplementary data for: A revision of the New Zealand weevil genus Irenimus Pascoe, 1876 (Coleoptera: Curculionidae: Entiminae).

description: This fileset contains DNA alignments, analysis scripts and Euler/X input files associated with the taxonomic revision "A revision of the New Zealand weevil genus <i>Irenimus</i> Pascoe, 1876 (Coleoptera: Curculionidae: Entiminae)" (Brown SDJ (2017). Zootaxa 4263(1): 1-42. doi: 10.11646/zootaxa.4263.1.1)<br><br><br><b>DNA alignment files in FASTA format:</b><br><i>coi.fasta</i>: 3' end of the cytochrome oxidase I mitochondrial gene (799 bp, 16 sequences)<br><i>coib.fasta</i>: 5' end ("barcoding region") of the cytochrome oxidase I mitochondrial gene (669 bp, 7 sequences)<br><i>28s.fasta</i>: D2-D3 region of 28S ribosomal RNA gene (756 bp, 17 sequences)<br><i>argk.fasta</i>: arginine kinase nuclear gene (715 bp, 17 sequences) <br><i>cad.fasta</i>: CAD nuclear gene (460 bp, 12 sequences)<br><br><b>Analysis scripts:<br></b><i>IrenimusMolecularDiagnostics.R</i>: Script file containing R code for creating the figures in the "Molecular Diagnostics" section of the paper.<b><br><br>Spreadsheet:<br></b><i>IrenimusData.csv</i>: comma separated table containing transcribed label data, georeferenced localities, and morphological data. Fields follow Darwin Core standards for geographic and label data. Morphological data fields are somewhat more idiosyncratic, but were intended to be self-explanatory.<br><br><b>Euler/X taxonomic alignment files:<br></b><i>Broun_Kuschel.txt</i>: Euler/X input file stating the articulations between the concepts of <i>Catoptes</i> sec. Broun and <i>Irenimus</i> sec. Kuschel.<br><i>Broun_Kuschel.pdf</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Broun_Kuschel.txt. This is a PDF version of Figure 97 in the paper. <br><i>Broun_Kuschel.svg</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Broun_Kuschel.txt. This is a SVG version of Figure 97 in the paper. <br><br><i>Brown_Broun.txt</i>: Euler/X input file stating the articulations between the concepts of <i>Catoptes</i> sec. Broun and <i>Chalepistes</i> sec. Brown.<br><i>Brown_Broun.pdf</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Brown_Broun.txt. This is a PDF version of Figure 98 in the paper. <br><i>Brown_Broun.svg</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Brown_Broun.txt. This is a SVG version of Figure 98 in the paper. <br><br><i>Kuschel_Brown.txt</i>: Euler/X input file stating the articulations between the concepts of <i>Irenimus</i> sec. Kuschel and <i>Chalepistes</i> sec. Brown.<br><i>Kuschel_Brown.pdf</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Kuschel_Brown.txt. This is a PDF version of Figure 99 in the paper. <br><i>Kuschel_Brown.svg</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Kuschel_Brown.txt. This is a SVG version of Figure 99 in the paper. <br>
DOI: 10.6084/m9.figshare.4600645.v1
title: Supplementary data for: A revision of the New Zealand weevil genus Irenimus Pascoe, 1876 (Coleoptera: Curculionidae: Entiminae).

description: This fileset contains DNA alignments, analysis scripts and Euler/X input files associated with the taxonomic revision "A revision of the New Zealand weevil genus <i>Irenimus</i> Pascoe, 1876 (Coleoptera: Curculionidae: Entiminae)" (Brown SDJ (2017). Zootaxa 4263(1): 1-42. doi: 10.11646/zootaxa.4263.1.1)<br><br><br><b>DNA alignment files in FASTA format:</b><br><i>coi.fasta</i>: 3' end of the cytochrome oxidase I mitochondrial gene (799 bp, 16 sequences)<br><i>coib.fasta</i>: 5' end ("barcoding region") of the cytochrome oxidase I mitochondrial gene (669 bp, 7 sequences)<br><i>28s.fasta</i>: D2-D3 region of 28S ribosomal RNA gene (756 bp, 17 sequences)<br><i>argk.fasta</i>: arginine kinase nuclear gene (715 bp, 17 sequences) <br><i>cad.fasta</i>: CAD nuclear gene (460 bp, 12 sequences)<br><br><b>Analysis scripts:<br></b><i>IrenimusMolecularDiagnostics.R</i>: Script file containing R code for creating the figures in the "Molecular Diagnostics" section of the paper.<b><br><br>Spreadsheet:<br></b><i>IrenimusData.csv</i>: comma separated table containing transcribed label data, georeferenced localities, and morphological data. Fields follow Darwin Core standards for geographic and label data. Morphological data fields are somewhat more idiosyncratic, but were intended to be self-explanatory.<br><br><b>Euler/X taxonomic alignment files:<br></b><i>Broun_Kuschel.txt</i>: Euler/X input file stating the articulations between the concepts of <i>Catoptes</i> sec. Broun and <i>Irenimus</i> sec. Kuschel.<br><i>Broun_Kuschel.pdf</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Broun_Kuschel.txt. This is a PDF version of Figure 97 in the paper. <br><i>Broun_Kuschel.svg</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Broun_Kuschel.txt. This is a SVG version of Figure 97 in the paper. <br><br><i>Brown_Broun.txt</i>: Euler/X input file stating the articulations between the concepts of <i>Catoptes</i> sec. Broun and <i>Chalepistes</i> sec. Brown.<br><i>Brown_Broun.pdf</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Brown_Broun.txt. This is a PDF version of Figure 98 in the paper. <br><i>Brown_Broun.svg</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Brown_Broun.txt. This is a SVG version of Figure 98 in the paper. <br><br><i>Kuschel_Brown.txt</i>: Euler/X input file stating the articulations between the concepts of <i>Irenimus</i> sec. Kuschel and <i>Chalepistes</i> sec. Brown.<br><i>Kuschel_Brown.pdf</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Kuschel_Brown.txt. This is a PDF version of Figure 99 in the paper. <br><i>Kuschel_Brown.svg</i>: Visualisation of the taxonomic concept alignment resulting from the articulations given in Kuschel_Brown.txt. This is a SVG version of Figure 99 in the paper. <br>
DOI: 10.6084/m9.figshare.4600420.v1
title: Hungate_qSIP_metadata.xlsx

description: This excel file contains metadata associated with MG-RAST project hungate_qSIP (mgp14151). It contains data on gene abundance (16S rRNA via quantitative PCR), fraction density, fraction DNA concentration, and other descriptive information.
DOI: 10.6084/m9.figshare.4600348
title: Relevance of meniscal cell regional phenotype to tissue engineering

description: <b><i>Purpose</i>:</b> Meniscus contains heterogeneous populations of cells that have not been fully characterized. Cell phenotype is often lost during culture; however, culture expansion is typically required for tissue engineering. We examined and compared cell-surface molecule expression levels on human meniscus cells from the vascular and avascular regions and articular chondrocytes while documenting changes during culture-induced dedifferentiation. <b><i>Materials and Methods</i>:</b> Expressions of 16 different surface molecules were examined by flow cytometry after monolayer culture for 24 h, 1 week, and 2 weeks. Menisci were also immunostained to document the spatial distributions of selected surface molecules. <b><i>Results</i>:</b> Meniscus cells and chondrocytes exhibited several similarities in surface molecule profiles with dynamic changes during culture. A greater percentage of meniscal cells were positive for CD14, CD26, CD49c, and CD49f compared to articular chondrocytes. Initially, more meniscal cells from the vascular region were positive for CD90 compared to cells from the avascular region or chondrocytes. Cells from the vascular region also expressed higher levels of CD166 and CD271 compared to cells from the avascular region. CD90, CD166, and CD271-positive cells were predominately perivascular in location. However, CD166-positive cells were also located in the superficial layer and in the adjacent synovial and adipose tissue. <b><i>Conclusions</i>:</b> These surface marker profiles provide a target phenotype for differentiation of progenitors in tissue engineering. The spatial location of progenitor cells in meniscus is consistent with higher regenerative capacity of the vascular region, while the surface progenitor subpopulations have potential to be utilized in tears created in the avascular region.
DOI: 10.6084/m9.figshare.4600348.v1
title: Relevance of meniscal cell regional phenotype to tissue engineering

description: <b><i>Purpose</i>:</b> Meniscus contains heterogeneous populations of cells that have not been fully characterized. Cell phenotype is often lost during culture; however, culture expansion is typically required for tissue engineering. We examined and compared cell-surface molecule expression levels on human meniscus cells from the vascular and avascular regions and articular chondrocytes while documenting changes during culture-induced dedifferentiation. <b><i>Materials and Methods</i>:</b> Expressions of 16 different surface molecules were examined by flow cytometry after monolayer culture for 24 h, 1 week, and 2 weeks. Menisci were also immunostained to document the spatial distributions of selected surface molecules. <b><i>Results</i>:</b> Meniscus cells and chondrocytes exhibited several similarities in surface molecule profiles with dynamic changes during culture. A greater percentage of meniscal cells were positive for CD14, CD26, CD49c, and CD49f compared to articular chondrocytes. Initially, more meniscal cells from the vascular region were positive for CD90 compared to cells from the avascular region or chondrocytes. Cells from the vascular region also expressed higher levels of CD166 and CD271 compared to cells from the avascular region. CD90, CD166, and CD271-positive cells were predominately perivascular in location. However, CD166-positive cells were also located in the superficial layer and in the adjacent synovial and adipose tissue. <b><i>Conclusions</i>:</b> These surface marker profiles provide a target phenotype for differentiation of progenitors in tissue engineering. The spatial location of progenitor cells in meniscus is consistent with higher regenerative capacity of the vascular region, while the surface progenitor subpopulations have potential to be utilized in tears created in the avascular region.
DOI: 10.6084/m9.figshare.4600336
title: Interprofessional spanning and building boundaries when supporting potential embryo donors to stem cell research

description: When patients undergo fertility treatment, it is likely that a surplus of embryos will be created. The existence of these surplus embryos creates responsibilities for the clinics where they are stored and for the people who own them. Since 2001, the owners of the surplus embryos in the UK have the option to donate them to be used in stem cell research (SCR). This development has generated a new population—<i>potential</i> embryo donors to SCR—who have unique support needs as they are neither fertility patients nor donors. However, little is known how lay and professional stakeholders associated with fertility treatment and SCR have conceptualised the support needs of potential embryo donors to SCR or have responded to the additional task once the option became available. In this article, we draw on Gieryn’s concept of boundary-work to explore how the emergence of donating embryos to SCR has provided opportunities for embryologists, counsellors, and scientists to shift, adapt, or confirm their roles, knowledge base, and areas of expertise. We present a thematic analysis of 21 in-depth, semi-structured interviews conducted with UK lay and professional stakeholders associated with fertility treatment and SCR. We conclude with reflections on the implications this boundary-work has for those contemplating donating embryos to SCR and the care they receive when making their decision. Such insights are pertinent given the current policy and practice discussions led by the National Donation Strategy Group to improve the care of donors in the UK.
DOI: 10.6084/m9.figshare.4600339
title: MRI scan data

description: MRI scan BMP format image slices (.zip archive) from this paper:Chadwick, KP; Shefelbine, SJ; Pitsillides, AA; Hutchinson, JR. 2017. Finite-element modelling of mechanobiological factors influencing sesamoid tissue morphology in the patellartendon of an ostrich. R. Soc. opensci. 4:170133. http://dx.doi.org/10.1098/rsos.170133
DOI: 10.6084/m9.figshare.4600336.v1
title: Interprofessional spanning and building boundaries when supporting potential embryo donors to stem cell research

description: When patients undergo fertility treatment, it is likely that a surplus of embryos will be created. The existence of these surplus embryos creates responsibilities for the clinics where they are stored and for the people who own them. Since 2001, the owners of the surplus embryos in the UK have the option to donate them to be used in stem cell research (SCR). This development has generated a new population—<i>potential</i> embryo donors to SCR—who have unique support needs as they are neither fertility patients nor donors. However, little is known how lay and professional stakeholders associated with fertility treatment and SCR have conceptualised the support needs of potential embryo donors to SCR or have responded to the additional task once the option became available. In this article, we draw on Gieryn’s concept of boundary-work to explore how the emergence of donating embryos to SCR has provided opportunities for embryologists, counsellors, and scientists to shift, adapt, or confirm their roles, knowledge base, and areas of expertise. We present a thematic analysis of 21 in-depth, semi-structured interviews conducted with UK lay and professional stakeholders associated with fertility treatment and SCR. We conclude with reflections on the implications this boundary-work has for those contemplating donating embryos to SCR and the care they receive when making their decision. Such insights are pertinent given the current policy and practice discussions led by the National Donation Strategy Group to improve the care of donors in the UK.