cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.926507
title: Mouse Whole Brain Interactome

description: Interactome was reverse engineered with ARACNe from a mouse whole brain expression dataset (437 samples, GSE10415). ARACNe was run with 100 bootstrap iterations using all probes that mapped to a set of 1,507 mouse transcriptional regulators (defined as genes annotated in the Gene Ontology Molecular Function database as GO:0003700 - ‘transcription factor activity’) for the human dataset. Parameters were set to 0 DPI tolerance and a MI P value threshold (P&lt;10-7), as recommended for bootstrap ARACNe analysis of a dataset with this size, to achieve a Bonferroni corrected significance (P = 0.05) for getting a single false-positive in the dataset.
DOI: 10.6084/m9.figshare.928091.v3
title: Data used in Gray et al. 2014 Dung beetles in riparian reserves Ecology and Evolution, In Press

description: Data used in Gray et al. 2014 Do riparian reserves support dung beetle biodiversity and ecosystem services in oil-palm dominated tropical landscapes Ecology and Evolution, In Press
DOI: 10.6084/m9.figshare.926486
title: Revision of the fossil rodent <i>Acaremys</i> Ameghino, 1887 (Hystricognathi, Octodontoidea, Acaremyidae) from the Miocene of Patagonia (Argentina) and the description of a new acaremyid

description: Within South American rodents, the Acaremyidae is an independent fossil lineage of octodontoids represented in the late Oligocene–middle Miocene of Patagonia. <i>Acaremys</i> is represented by six species recorded in the early Miocene, which have not been re-studied since their original description. Morphological and phylogenetic analyses suggest that <i>Acaremys</i> is paraphyletic. Three species are valid, <i>Acaremys</i><i>murinus</i>, <i>Acaremys</i><i>major</i>, and <i>Acaremys</i><i>messor</i>. <i>Acaremys</i><i>karaikensis</i> is a junior synonym of <i>Acaremys</i><i>murinus</i>. ‘<i>Acaremys</i>’ <i>tricarinatus</i> is excluded from the genus being closely related to <i>Sciamys</i>. The new species, <i>Pseudoacaremys kramarzi</i>, is closely related to ‘<i>Acaremys</i>’ <i>tricarinatus</i> and <i>Sciamys</i>. ‘<i>Acaremys</i>’ <i>preminutus</i> is excluded from the family being closely related to the early Miocene <i>Protacaremys prior</i>, or living octodontoids. The phylogenetic analysis demonstrated that Acaremyidae includes <i>Platypittamys</i>, <i>Galileomys</i>, <i>Acaremys</i>, <i>Pseudoacaremys</i> and <i>Sciamys</i>. The new acaremyid increases the diversity of extinct octodontoids and added a new evolutionary lineage within Acaremyidae. The evolutionary history of the superfamily suggests that the hypsodonty and the consequently occlusal simplification evolved twice within Octodontoidea: in Acaremyidae and in Octodontidae. In addition, the cladistic analysis confirmed that most character ambiguities are due to missing data, and hence, it is essential to find better remains to elucidate the relationships among acaremyids.
DOI: 10.6084/m9.figshare.926487
title: Gaussian Job Archive for C33H27CuI2N3P

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.926485
title: Supplementary data files for "Archaeal 'dark matter' and the origin of eukaryotes"

description: This is the supplementary data file associated with Williams and Embley (2014) GBE "Archaeal 'dark matter' and the origin of eukaryotes". It includes the alignments and tree files generated as part of the analysis.
DOI: 10.6084/m9.figshare.926485.v1
title: Supplementary data files for "Archaeal 'dark matter' and the origin of eukaryotes"

description: This is the supplementary data file associated with Williams and Embley (2014) GBE "Archaeal 'dark matter' and the origin of eukaryotes". It includes the alignments and tree files generated as part of the analysis.
DOI: 10.6084/m9.figshare.928091.v4
title: Data used in Gray et al. 2014 Dung beetles in riparian reserves Ecology and Evolution, In Press

description: Data used in Gray et al. 2014 Do riparian reserves support dung beetle biodiversity and ecosystem services in oil-palm dominated tropical landscapes Ecology and Evolution, In Press
DOI: 10.6084/m9.figshare.926487.v1
title: Gaussian Job Archive for C33H27CuI2N3P

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.926462
title: Empria asiatica Muche, 1965, types

description: <em><strong>Empria asiatica</strong></em> Muche, 1965, types holotype, GBIF-GISHym2376 paratype, paratypus_01 paratype, paratypus_02
DOI: 10.6084/m9.figshare.928091.v5
title: Data used in Gray et al. 2014 Dung beetles in riparian reserves Ecology and Evolution, In Press

description: Data used in Gray et al. 2014 Do riparian reserves support dung beetle biodiversity and ecosystem services in oil-palm dominated tropical landscapes Ecology and Evolution
DOI: 10.6084/m9.figshare.926462.v1
title: Empria asiatica Muche, 1965, types

description: <em><strong>Empria asiatica</strong></em> Muche, 1965, types holotype, GBIF-GISHym2376 paratype, paratypus_01 paratype, paratypus_02
DOI: 10.6084/m9.figshare.926486.v1
title: Revision of the fossil rodent <i>Acaremys</i> Ameghino, 1887 (Hystricognathi, Octodontoidea, Acaremyidae) from the Miocene of Patagonia (Argentina) and the description of a new acaremyid

description: Within South American rodents, the Acaremyidae is an independent fossil lineage of octodontoids represented in the late Oligocene–middle Miocene of Patagonia. <i>Acaremys</i> is represented by six species recorded in the early Miocene, which have not been re-studied since their original description. Morphological and phylogenetic analyses suggest that <i>Acaremys</i> is paraphyletic. Three species are valid, <i>Acaremys</i><i>murinus</i>, <i>Acaremys</i><i>major</i>, and <i>Acaremys</i><i>messor</i>. <i>Acaremys</i><i>karaikensis</i> is a junior synonym of <i>Acaremys</i><i>murinus</i>. ‘<i>Acaremys</i>’ <i>tricarinatus</i> is excluded from the genus being closely related to <i>Sciamys</i>. The new species, <i>Pseudoacaremys kramarzi</i>, is closely related to ‘<i>Acaremys</i>’ <i>tricarinatus</i> and <i>Sciamys</i>. ‘<i>Acaremys</i>’ <i>preminutus</i> is excluded from the family being closely related to the early Miocene <i>Protacaremys prior</i>, or living octodontoids. The phylogenetic analysis demonstrated that Acaremyidae includes <i>Platypittamys</i>, <i>Galileomys</i>, <i>Acaremys</i>, <i>Pseudoacaremys</i> and <i>Sciamys</i>. The new acaremyid increases the diversity of extinct octodontoids and added a new evolutionary lineage within Acaremyidae. The evolutionary history of the superfamily suggests that the hypsodonty and the consequently occlusal simplification evolved twice within Octodontoidea: in Acaremyidae and in Octodontidae. In addition, the cladistic analysis confirmed that most character ambiguities are due to missing data, and hence, it is essential to find better remains to elucidate the relationships among acaremyids.
DOI: 10.6084/m9.figshare.928091.v7
title: Data used in Gray et al. 2014 Dung beetles in riparian reserves Ecology and Evolution

description: Data used in Gray et al. 2014 Do riparian reserves support dung beetle biodiversity and ecosystem services in oil-palm dominated tropical landscapes Ecology and Evolution
DOI: 10.6084/m9.figshare.926486.v2
title: Revision of the fossil rodent <i>Acaremys</i> Ameghino, 1887 (Hystricognathi, Octodontoidea, Acaremyidae) from the Miocene of Patagonia (Argentina) and the description of a new acaremyid

description: Within South American rodents, the Acaremyidae is an independent fossil lineage of octodontoids represented in the late Oligocene–middle Miocene of Patagonia. <i>Acaremys</i> is represented by six species recorded in the early Miocene, which have not been re-studied since their original description. Morphological and phylogenetic analyses suggest that <i>Acaremys</i> is paraphyletic. Three species are valid, <i>Acaremys</i><i>murinus</i>, <i>Acaremys</i><i>major</i>, and <i>Acaremys</i><i>messor</i>. <i>Acaremys</i><i>karaikensis</i> is a junior synonym of <i>Acaremys</i><i>murinus</i>. ‘<i>Acaremys</i>’ <i>tricarinatus</i> is excluded from the genus being closely related to <i>Sciamys</i>. The new species, <i>Pseudoacaremys kramarzi</i>, is closely related to ‘<i>Acaremys</i>’ <i>tricarinatus</i> and <i>Sciamys</i>. ‘<i>Acaremys</i>’ <i>preminutus</i> is excluded from the family being closely related to the early Miocene <i>Protacaremys prior</i>, or living octodontoids. The phylogenetic analysis demonstrated that Acaremyidae includes <i>Platypittamys</i>, <i>Galileomys</i>, <i>Acaremys</i>, <i>Pseudoacaremys</i> and <i>Sciamys</i>. The new acaremyid increases the diversity of extinct octodontoids and added a new evolutionary lineage within Acaremyidae. The evolutionary history of the superfamily suggests that the hypsodonty and the consequently occlusal simplification evolved twice within Octodontoidea: in Acaremyidae and in Octodontidae. In addition, the cladistic analysis confirmed that most character ambiguities are due to missing data, and hence, it is essential to find better remains to elucidate the relationships among acaremyids.
DOI: 10.6084/m9.figshare.928091.v6
title: Data used in Gray et al. 2014 Dung beetles in riparian reserves Ecology and Evolution

description: Data used in Gray et al. 2014 Do riparian reserves support dung beetle biodiversity and ecosystem services in oil-palm dominated tropical landscapes Ecology and Evolution
DOI: 10.6084/m9.figshare.926486.v4
title: Revision of the fossil rodent <i>Acaremys</i> Ameghino, 1887 (Hystricognathi, Octodontoidea, Acaremyidae) from the Miocene of Patagonia (Argentina) and the description of a new acaremyid

description: Within South American rodents, the Acaremyidae is an independent fossil lineage of octodontoids represented in the late Oligocene–middle Miocene of Patagonia. <i>Acaremys</i> is represented by six species recorded in the early Miocene, which have not been re-studied since their original description. Morphological and phylogenetic analyses suggest that <i>Acaremys</i> is paraphyletic. Three species are valid, <i>Acaremys</i><i>murinus</i>, <i>Acaremys</i><i>major</i>, and <i>Acaremys</i><i>messor</i>. <i>Acaremys</i><i>karaikensis</i> is a junior synonym of <i>Acaremys</i><i>murinus</i>. ‘<i>Acaremys</i>’ <i>tricarinatus</i> is excluded from the genus being closely related to <i>Sciamys</i>. The new species, <i>Pseudoacaremys kramarzi</i>, is closely related to ‘<i>Acaremys</i>’ <i>tricarinatus</i> and <i>Sciamys</i>. ‘<i>Acaremys</i>’ <i>preminutus</i> is excluded from the family being closely related to the early Miocene <i>Protacaremys prior</i>, or living octodontoids. The phylogenetic analysis demonstrated that Acaremyidae includes <i>Platypittamys</i>, <i>Galileomys</i>, <i>Acaremys</i>, <i>Pseudoacaremys</i> and <i>Sciamys</i>. The new acaremyid increases the diversity of extinct octodontoids and added a new evolutionary lineage within Acaremyidae. The evolutionary history of the superfamily suggests that the hypsodonty and the consequently occlusal simplification evolved twice within Octodontoidea: in Acaremyidae and in Octodontidae. In addition, the cladistic analysis confirmed that most character ambiguities are due to missing data, and hence, it is essential to find better remains to elucidate the relationships among acaremyids.
DOI: 10.6084/m9.figshare.924807
title: Supplementary Figure 1. Illustration of the metagenome binning signal provided by Hi-C.

description: Two bacterial cells are illustrated, each containing a single circular chromosome. For one genomic region in each of the two species, examples of associations that are likely (green; red is “not likely”) to be derived from Hi-C are illustrated.
DOI: 10.6084/m9.figshare.924807.v1
title: Supplementary Figure 1. Illustration of the metagenome binning signal provided by Hi-C.

description: Two bacterial cells are illustrated, each containing a single circular chromosome. For one genomic region in each of the two species, examples of associations that are likely (green; red is “not likely”) to be derived from Hi-C are illustrated.
DOI: 10.6084/m9.figshare.926486.v3
title: Revision of the fossil rodent <i>Acaremys</i> Ameghino, 1887 (Hystricognathi, Octodontoidea, Acaremyidae) from the Miocene of Patagonia (Argentina) and the description of a new acaremyid

description: Within South American rodents, the Acaremyidae is an independent fossil lineage of octodontoids represented in the late Oligocene–middle Miocene of Patagonia. <i>Acaremys</i> is represented by six species recorded in the early Miocene, which have not been re-studied since their original description. Morphological and phylogenetic analyses suggest that <i>Acaremys</i> is paraphyletic. Three species are valid, <i>Acaremys</i><i>murinus</i>, <i>Acaremys</i><i>major</i>, and <i>Acaremys</i><i>messor</i>. <i>Acaremys</i><i>karaikensis</i> is a junior synonym of <i>Acaremys</i><i>murinus</i>. ‘<i>Acaremys</i>’ <i>tricarinatus</i> is excluded from the genus being closely related to <i>Sciamys</i>. The new species, <i>Pseudoacaremys kramarzi</i>, is closely related to ‘<i>Acaremys</i>’ <i>tricarinatus</i> and <i>Sciamys</i>. ‘<i>Acaremys</i>’ <i>preminutus</i> is excluded from the family being closely related to the early Miocene <i>Protacaremys prior</i>, or living octodontoids. The phylogenetic analysis demonstrated that Acaremyidae includes <i>Platypittamys</i>, <i>Galileomys</i>, <i>Acaremys</i>, <i>Pseudoacaremys</i> and <i>Sciamys</i>. The new acaremyid increases the diversity of extinct octodontoids and added a new evolutionary lineage within Acaremyidae. The evolutionary history of the superfamily suggests that the hypsodonty and the consequently occlusal simplification evolved twice within Octodontoidea: in Acaremyidae and in Octodontidae. In addition, the cladistic analysis confirmed that most character ambiguities are due to missing data, and hence, it is essential to find better remains to elucidate the relationships among acaremyids.
DOI: 10.6084/m9.figshare.924800
title: Data from "Water flow and fin-shape polymorphism in coral reef fishes:

description: Data from Binning & Roche 2015 (Ecology: 10.1890/14-0426.1) This study evaluated the generality of intraspecific phenotypic divergence in widespread coral reef fishes by exploring patterns of fin shape divergence in 12 common species from three families of pectoral fin swimming (labriform) fishes on the Great Barrier Reef. This study was conducted between March 2010 and August 2013 at sites around Lizard Island, on the northern Great Barrier Reef, Australia. Three sites located on reef crest habitats (2- 4 m depth) were chosen on the windward (wave exposed) and three sites on the leeward (sheltered) side of the island. In addition, two sites each on the reef slope (8 -10 m depth), crest (2 – 4 m depth) and back lagoon (1 – 2 m depth) were chosen on the windward side of the island. Fishes were collected with hand spears or barrier nets. Fish total length was measured with a ruler, and fin AR was calculated as the length of the leading edge squared divided by the total fin area. The abundance of adults fishes from the 12 species was recorded at all study sites by SCUBA divers using underwater belt transects (50 × 4 m). All adult individuals (displaying adult coloration and/or &gt; 5 cm total length) were counted for each species in four replicate transects at each site covering 800 m2 of habitat per site. Please see Binning & Roche 2015 (10.1890/14-0426.1) for more detailed description of the methods.
DOI: 10.6084/m9.figshare.924797
title: Merged: NCI Thesaurus, selected openEHR archetypes and test patient data

description: File contains test patient data, represented as instances of selected openEHR archetypes [1], translated to owl. Additionally the file contains merged NCI Thesaurus [2]. File was generated in order to demonstrate how to transform structured eligibility criteria of clinical trials to SPARQL queries. The example queries [3] utilize the hierarchy of NCI thesaurus. The file accompanies the publication [4]. The translation of archetypes from adl to owl was done using the methods defined by L.Lezcano and K. Dentler [4,5].
DOI: 10.6084/m9.figshare.924793
title: dsIDR

description: dsIDR legal notes
DOI: 10.6084/m9.figshare.924796
title: Template eligibility queries in SPARQL

description: File contains template SPARQL queries corresponding to specif types of eligibility criteria of clincial trials. Queries can be used to explore the linked test patient data.
DOI: 10.6084/m9.figshare.924797.v1
title: Merged: NCI Thesaurus, selected openEHR archetypes and test patient data

description: File contains test patient data, represented as instances of selected openEHR archetypes [1], translated to owl. Additionally the file contains merged NCI Thesaurus [2]. File was generated in order to demonstrate how to transform structured eligibility criteria of clinical trials to SPARQL queries. The example queries [3] utilize the hierarchy of NCI thesaurus. The file accompanies the publication [4]. The translation of archetypes from adl to owl was done using the methods defined by L.Lezcano and K. Dentler [4,5].
DOI: 10.6084/m9.figshare.924740
title: A new compendium of soil respiration data for Africa

description: Soil Respiration, Database, Africa
DOI: 10.6084/m9.figshare.924792
title: Stimuli list - Social influence on risk perception during adolescence

description: Stimuli list for experiment"are you a risk-taker?" 2013. published: Title: Social influence on risk perception during adolescence Authors: Lisa J. Knoll1*, Lucía Magis-Weinberg2, Maarten Speekenbrink2 and Sarah-Jayne Blakemore1 In press in Psychological Science.
DOI: 10.6084/m9.figshare.924800.v1
title: Data from Binning & Roche In Review

description: Data from Binning & Roche In review This study evaluated the generality of intraspecific phenotypic divergence in widespread coral reef fishes by exploring patterns of fin shape divergence in 12 common species from three families of pectoral fin swimming (labriform) fishes on the Great Barrier Reef. This study was conducted between March 2010 and August 2013 at sites around Lizard Island, on the northern Great Barrier Reef, Australia. Three sites located on reef crest habitats (2- 4 m depth) were chosen on the windward (wave exposed) and three sites on the leeward (sheltered) side of the island. In addition, two sites each on the reef slope (8 -10 m depth), crest (2 – 4 m depth) and back lagoon (1 – 2 m depth) were chosen on the windward side of the island. Fishes were collected with hand spears or barrier nets. Fish total length was measured with a ruler, and fin AR was calculated as the length of the leading edge squared divided by the total fin area. The abundance of adults fishes from the 12 species was recorded at all study sites by SCUBA divers using underwater belt transects (50 × 4 m). All adult individuals (displaying adult coloration and/or &gt; 5 cm total length) were counted for each species in four replicate transects at each site covering 800 m2 of habitat per site. Please see Binning & Roche for more detailed description of the methods.
DOI: 10.6084/m9.figshare.924800.v3
title: Data from "Water flow and fin-shape polymorphism in coral reef fishes:

description: Data from Binning & Roche 2015 (Ecology: 10.1890/14-0426.1) This study evaluated the generality of intraspecific phenotypic divergence in widespread coral reef fishes by exploring patterns of fin shape divergence in 12 common species from three families of pectoral fin swimming (labriform) fishes on the Great Barrier Reef. This study was conducted between March 2010 and August 2013 at sites around Lizard Island, on the northern Great Barrier Reef, Australia. Three sites located on reef crest habitats (2- 4 m depth) were chosen on the windward (wave exposed) and three sites on the leeward (sheltered) side of the island. In addition, two sites each on the reef slope (8 -10 m depth), crest (2 – 4 m depth) and back lagoon (1 – 2 m depth) were chosen on the windward side of the island. Fishes were collected with hand spears or barrier nets. Fish total length was measured with a ruler, and fin AR was calculated as the length of the leading edge squared divided by the total fin area. The abundance of adults fishes from the 12 species was recorded at all study sites by SCUBA divers using underwater belt transects (50 × 4 m). All adult individuals (displaying adult coloration and/or &gt; 5 cm total length) were counted for each species in four replicate transects at each site covering 800 m2 of habitat per site. Please see Binning & Roche 2015 (10.1890/14-0426.1) for more detailed description of the methods.
DOI: 10.6084/m9.figshare.924733
title: Average Surfers

description: Very Average Surfers from the ASP World Tour: 2013 These images show a population average of the female and male world tour surfers from 2013. Computed with Advanced Normalization Tools in R (ANTsR).
DOI: 10.6084/m9.figshare.924793.v1
title: dsIDR

description: dsIDR legal notes
DOI: 10.6084/m9.figshare.924792.v1
title: Stimuli list - Social influence on risk perception during adolescence

description: Stimuli list for study "are you a risk-taker?" 2013. Study "Social influence on risk perception during adolescence"
DOI: 10.6084/m9.figshare.924792.v2
title: Stimuli list - Social influence on risk perception during adolescence

description: Stimuli list for experiment"are you a risk-taker?" 2013. published: Title: Social influence on risk perception during adolescence Authors: Lisa J. Knoll1*, Lucía Magis-Weinberg2, Maarten Speekenbrink2 and Sarah-Jayne Blakemore1 In press in Psychological Science.
DOI: 10.6084/m9.figshare.924800.v2
title: Data from Binning & Roche In Review

description: Data from Binning & Roche In review This study evaluated the generality of intraspecific phenotypic divergence in widespread coral reef fishes by exploring patterns of fin shape divergence in 12 common species from three families of pectoral fin swimming (labriform) fishes on the Great Barrier Reef. This study was conducted between March 2010 and August 2013 at sites around Lizard Island, on the northern Great Barrier Reef, Australia. Three sites located on reef crest habitats (2- 4 m depth) were chosen on the windward (wave exposed) and three sites on the leeward (sheltered) side of the island. In addition, two sites each on the reef slope (8 -10 m depth), crest (2 – 4 m depth) and back lagoon (1 – 2 m depth) were chosen on the windward side of the island. Fishes were collected with hand spears or barrier nets. Fish total length was measured with a ruler, and fin AR was calculated as the length of the leading edge squared divided by the total fin area. The abundance of adults fishes from the 12 species was recorded at all study sites by SCUBA divers using underwater belt transects (50 × 4 m). All adult individuals (displaying adult coloration and/or &gt; 5 cm total length) were counted for each species in four replicate transects at each site covering 800 m2 of habitat per site. Please see Binning & Roche for more detailed description of the methods.
DOI: 10.6084/m9.figshare.924740.v1
title: Mr

description: This dataset is the first most comprehensive dataset on soil respiration in Africa. It present raw data on 52 observations obtained through meta analysis from over 28 different publications. Prior to this dataset, the only other dataset that existed had just 4 observations of soil respiration for the entire African continent.
DOI: 10.6084/m9.figshare.924793.v3
title: dsIDR

description: dsIDR legal notes
DOI: 10.6084/m9.figshare.924733.v2
title: Average Surfers

description: Very Average Surfers from the ASP World Tour: 2013 These images show a population average of the female and male world tour surfers from 2013. Computed with Advanced Normalization Tools in R (ANTsR).
DOI: 10.6084/m9.figshare.924733.v1
title: new fileset

description: Very Average Surfers from the ASP World Tour: 2013 These images show a population average of the female and male world tour surfers from 2013. Computed with Advanced Normalization Tools in R (ANTsR).