cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1048856.v2
title: Comparison of Paired ROC Curves through a Two-Stage Test

description: The area under the receiver operating characteristic (ROC) curve (AUC) is a popularly used index when comparing two ROC curves. Statistical tests based on it for analyzing the difference have been well developed. However, this index is less informative when two ROC curves cross and have similar AUCs. In order to detect differences between ROC curves in such situations, a two-stage nonparametric test that uses a shifted area under the ROC curve (sAUC), along with AUCs, is proposed for paired designs. The new procedure is shown, numerically, to be effective in terms of power under a wide range of scenarios; additionally, it outperforms two conventional ROC-type tests, especially when two ROC curves cross each other and have similar AUCs. Larger sAUC implies larger partial AUC at the range of low false-positive rates in this case. Because high specificity is important in many classification tasks, such as medical diagnosis, this is an appealing characteristic. The test also implicitly analyzes the equality of two commonly used binormal ROC curves at every operating point. We also apply the proposed method to synthesized data and two real examples to illustrate its usefulness in practice.
DOI: 10.6084/m9.figshare.1048856.v4
title: Comparison of Paired ROC Curves through a Two-Stage Test

description: The area under the receiver operating characteristic (ROC) curve (AUC) is a popularly used index when comparing two ROC curves. Statistical tests based on it for analyzing the difference have been well developed. However, this index is less informative when two ROC curves cross and have similar AUCs. In order to detect differences between ROC curves in such situations, a two-stage nonparametric test that uses a shifted area under the ROC curve (sAUC), along with AUCs, is proposed for paired designs. The new procedure is shown, numerically, to be effective in terms of power under a wide range of scenarios; additionally, it outperforms two conventional ROC-type tests, especially when two ROC curves cross each other and have similar AUCs. Larger sAUC implies larger partial AUC at the range of low false-positive rates in this case. Because high specificity is important in many classification tasks, such as medical diagnosis, this is an appealing characteristic. The test also implicitly analyzes the equality of two commonly used binormal ROC curves at every operating point. We also apply the proposed method to synthesized data and two real examples to illustrate its usefulness in practice.
DOI: 10.6084/m9.figshare.1048834
title: Continuum of land rights

description: Development of the land tenure continuum concept initially promoted by the UN Habitat
DOI: 10.6084/m9.figshare.1048856.v3
title: Comparison of Paired ROC Curves through a Two-Stage Test

description: The area under the receiver operating characteristic (ROC) curve (AUC) is a popularly used index when comparing two ROC curves. Statistical tests based on it for analyzing the difference have been well developed. However, this index is less informative when two ROC curves cross and have similar AUCs. In order to detect differences between ROC curves in such situations, a two-stage nonparametric test that uses a shifted area under the ROC curve (sAUC), along with AUCs, is proposed for paired designs. The new procedure is shown, numerically, to be effective in terms of power under a wide range of scenarios; additionally, it outperforms two conventional ROC-type tests, especially when two ROC curves cross each other and have similar AUCs. Larger sAUC implies larger partial AUC at the range of low false-positive rates in this case. Because high specificity is important in many classification tasks, such as medical diagnosis, this is an appealing characteristic. The test also implicitly analyzes the equality of two commonly used binormal ROC curves at every operating point. We also apply the proposed method to synthesized data and two real examples to illustrate its usefulness in practice.
DOI: 10.6084/m9.figshare.1048834.v2
title: Continuum of land rights

description: Development of the land tenure continuum concept initially promoted by the UN Habitat
DOI: 10.6084/m9.figshare.1048834.v1
title: Continuum of land rights

description: Development of the land tenure continuum concept initially promoted by the UN Habitat
DOI: 10.6084/m9.figshare.1048832
title: Integrated Coastal Management

description: Understanding the legal framework and various heighting datums in the coastal areas of South Africa
DOI: 10.6084/m9.figshare.1048832.v1
title: Integrated Coastal Management

description: Understanding the legal framework and various heighting datums in the coastal areas of South Africa
DOI: 10.6084/m9.figshare.1048829
title: Trimmed and cleaned reads

description: Input reads to replicate WABI 2014 experiments
DOI: 10.6084/m9.figshare.1048829.v1
title: Trimmed and cleaned reads

description: Input reads to replicate WABI 2014 experiments
DOI: 10.6084/m9.figshare.1048832.v2
title: Integrated Coastal Management

description: Understanding the legal framework and various heighting datums in the coastal areas of South Africa
DOI: 10.6084/m9.figshare.1048832.v4
title: Integrated Coastal Management

description: Understanding the legal framework and various heighting datums in the coastal areas of South Africa
DOI: 10.6084/m9.figshare.1048761
title: Gaussian Job Archive for C16H16(5)

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1048832.v3
title: Integrated Coastal Management

description: Understanding the legal framework and various heighting datums in the coastal areas of South Africa
DOI: 10.6084/m9.figshare.1048760
title: Gaussian Job Archive for C16H16(3)

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1048761.v1
title: Gaussian Job Archive for C16H16(5)

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1048748
title: all_tRNA_genes_in_clusters.tsv

description: tRNA cluster definitions
DOI: 10.6084/m9.figshare.1048749
title: Gaussian Job Archive for C16H16

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1048749.v1
title: Gaussian Job Archive for C16H16

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1048748.v1
title: all_tRNA_genes_in_clusters.tsv

description: tRNA cluster definitions
DOI: 10.6084/m9.figshare.1047292
title: Get all pathways with a particular Pubmed reference

description: PREFIX wp: <br>PREFIX rdfs: <br>PREFIX dc: <br>PREFIX foaf: <br>PREFIX dcterms: SELECT DISTINCT ?wpUrl ?pubmed<br>WHERE<br>{?pubmed a wp:PublicationReference .<br>?pubmed dcterms:isPartOf ?pathway .<br>?pathway dc:identifier ?wpUrl .}<br>ORDER BY ?pathway
DOI: 10.6084/m9.figshare.1047288
title: Get all pathways with a particular gene

description: PREFIX wp: <br>PREFIX rdfs: <br>PREFIX dc: <br>PREFIX foaf: <br>PREFIX dcterms: SELECT DISTINCT ?pwUrl ?label where {<br>?geneProduct a wp:GeneProduct .<br>?geneProduct rdfs:label ?label .<br>?geneProduct dcterms:isPartOf ?pathway .<br>?pathway dc:identifier ?pwUrl . FILTER regex(str(?label), "CYP").<br>}
DOI: 10.6084/m9.figshare.1047288.v1
title: Get all pathways with a particular gene

description: PREFIX wp: <br>PREFIX rdfs: <br>PREFIX dc: <br>PREFIX foaf: <br>PREFIX dcterms: SELECT DISTINCT ?pwUrl ?label where {<br>?geneProduct a wp:GeneProduct .<br>?geneProduct rdfs:label ?label .<br>?geneProduct dcterms:isPartOf ?pathway .<br>?pathway dc:identifier ?pwUrl . FILTER regex(str(?label), "CYP").<br>}
DOI: 10.6084/m9.figshare.1047286
title: List all pathways for a given species (e.g. "Mus musculus")

description: PREFIX wp: <br>PREFIX rdfs: <br>PREFIX dc: <br>PREFIX foaf: SELECT DISTINCT ?wpIdentifier ?pathway ?page<br>WHERE {<br>?pathway dc:title ?title .<br>?pathway wp:organism ?organism .<br>?pathway foaf:page ?page .<br>?pathway dc:identifier ?wpIdentifier .<br>?organism rdfs:label "Mus musculus"^^ .<br>}<br>ORDER BY ?wpIdentifier
DOI: 10.6084/m9.figshare.1047292.v1
title: Get all pathways with a particular Pubmed reference

description: PREFIX wp: <br>PREFIX rdfs: <br>PREFIX dc: <br>PREFIX foaf: <br>PREFIX dcterms: SELECT DISTINCT ?wpUrl ?pubmed<br>WHERE<br>{?pubmed a wp:PublicationReference .<br>?pubmed dcterms:isPartOf ?pathway .<br>?pathway dc:identifier ?wpUrl .}<br>ORDER BY ?pathway
DOI: 10.6084/m9.figshare.1047279
title: A systematic review of the ecological literature on cushion plants

description: Cushion-forming plant species are found in alpine and polar environments around the world. They modify the microclimate, thereby facilitating other plant species. Similar to the effectiveness of shrubs as a means to study facilitation in arid and semi-arid environments, we explore the potential for cushion plant species to expand the general- ity of research on this contemporary ecological interaction. A systematic review was conducted to determine the number of publications and citation frequency on relevant ecological topics whilst using shrub literature as a baseline to assess relative importance of cushions as a focal point for future ecological research. Although, there are forty times more shrub articles, mean citations per paper is comparable between cushion and shrub literature. Furthermore, the scope of ecological research topics studied us- ing cushions is broad including facilitation, competition, environmental gradients, life history, genetics, reproduction, community, ecosystem and evolution. The preliminary ecological evidence to date also strongly suggests that cushion plants can be keystone species in their ecosystems. Hence, ecological research on net interactions including facilitation and patterns of diversity can be successfully examined using cushion plants, and this is particularly timely given expectations associated with a changing climate in these regions.
DOI: 10.6084/m9.figshare.1047283
title: List the species captured in WikiPathways and the number of pathways per species.

description: Example query to count the pathways per species in WikiPathways:<br><br>PREFIX wp: <br>PREFIX rdfs: <br>PREFIX dc: SELECT DISTINCT ?organism ?label count(?pathway) as ?noPathways<br>WHERE {<br>?pathway dc:title ?title .<br>?pathway wp:organism ?organism .<br>?organism rdfs:label ?label .<br>}<br>ORDER BY DESC(?noPathways)
DOI: 10.6084/m9.figshare.1047278
title: List the species captured in WikiPathways.

description: This is the example query to get the species covered in WikiPathways
DOI: 10.6084/m9.figshare.1047279.v1
title: A systematic review of the ecological literature on cushion plants

description: Cushion-forming plant species are found in alpine and polar environments around the world. They modify the microclimate, thereby facilitating other plant species. Similar to the effectiveness of shrubs as a means to study facilitation in arid and semi-arid environments, we explore the potential for cushion plant species to expand the general- ity of research on this contemporary ecological interaction. A systematic review was conducted to determine the number of publications and citation frequency on relevant ecological topics whilst using shrub literature as a baseline to assess relative importance of cushions as a focal point for future ecological research. Although, there are forty times more shrub articles, mean citations per paper is comparable between cushion and shrub literature. Furthermore, the scope of ecological research topics studied us- ing cushions is broad including facilitation, competition, environmental gradients, life history, genetics, reproduction, community, ecosystem and evolution. The preliminary ecological evidence to date also strongly suggests that cushion plants can be keystone species in their ecosystems. Hence, ecological research on net interactions including facilitation and patterns of diversity can be successfully examined using cushion plants, and this is particularly timely given expectations associated with a changing climate in these regions.
DOI: 10.6084/m9.figshare.1047286.v1
title: List all pathways for a given species (e.g. "Mus musculus")

description: PREFIX wp: <br>PREFIX rdfs: <br>PREFIX dc: <br>PREFIX foaf: SELECT DISTINCT ?wpIdentifier ?pathway ?page<br>WHERE {<br>?pathway dc:title ?title .<br>?pathway wp:organism ?organism .<br>?pathway foaf:page ?page .<br>?pathway dc:identifier ?wpIdentifier .<br>?organism rdfs:label "Mus musculus"^^ .<br>}<br>ORDER BY ?wpIdentifier
DOI: 10.6084/m9.figshare.1047283.v1
title: List the species captured in WikiPathways and the number of pathways per species.

description: Example query to count the pathways per species in WikiPathways:<br><br>PREFIX wp: <br>PREFIX rdfs: <br>PREFIX dc: SELECT DISTINCT ?organism ?label count(?pathway) as ?noPathways<br>WHERE {<br>?pathway dc:title ?title .<br>?pathway wp:organism ?organism .<br>?organism rdfs:label ?label .<br>}<br>ORDER BY DESC(?noPathways)
DOI: 10.6084/m9.figshare.1047263
title: Molecular Characterization of Prokaryotic Communities Associated with Lonar Crater Basalts

description: The Lonar crater is an unusually well-preserved meteorite impact structure that is located in one of the largest volcanic provinces on Earth (i.e., the Deccan Traps in India). The diversity of endoliths in Lonar crater basalts or Deccan flood basalts is not known. Here, the phylogenetic diversity of endolithic <i>Bacteria</i> and <i>Archaea</i> inhabiting basalts retrieved from four discrete sampling sites on the Lonar crater walls and the lake-bed was assessed using culture-independent molecular methods. Taxonomic classification of 16S rRNA gene sequences from all four basalt samples revealed similarities as well as dissimilarities in the presence or absence of several prokaryotic taxa. Cluster analysis of Denaturing gradient gel electrophoresis fingerprints and UniFrac analysis of clone library sequences suggested substantial variations in bacterial and archaeal diversity between crater-wall and lake-bed sites. Although sequences affiliated to the bacterial phyla <i>Actinobacteria</i>, <i>Acidobacteria</i> and <i>Chloroflexi</i> were relatively more abundant in crater-wall basalts than in lake-bed basalts; the reverse was observed for sequences related to <i>Proteobacteria</i>, <i>Firmicutes</i>, <i>Cyanobacteria</i> and <i>Bacteroidetes</i>. <i>Archaea</i> in crater-wall and lake-bed basalt libraries were almost completely represented by <i>Thaumarchaeota</i> and <i>Euryarchaeota</i>, respectively. Diversity indices and richness estimates suggested the diversity of endolithic <i>Bacteria</i> to be higher than that of <i>Archaea</i> in the Lonar crater basalts. A substantial number of clone library sequences did not affiliate with extant <i>Bacteria</i> and <i>Archaea</i>. The detection of several putative lineages associated with C, N and S cycling suggests that the Lonar crater basalts are colonized by metabolically diverse prokaryotic communities involved in biogeochemical cycling of major elements.
DOI: 10.6084/m9.figshare.1047278.v1
title: List the species captured in WikiPathways.

description: This is the example query to get the species covered in WikiPathways
DOI: 10.6084/m9.figshare.1047263.v2
title: Molecular Characterization of Prokaryotic Communities Associated with Lonar Crater Basalts

description: The Lonar crater is an unusually well-preserved meteorite impact structure that is located in one of the largest volcanic provinces on Earth (i.e., the Deccan Traps in India). The diversity of endoliths in Lonar crater basalts or Deccan flood basalts is not known. Here, the phylogenetic diversity of endolithic <i>Bacteria</i> and <i>Archaea</i> inhabiting basalts retrieved from four discrete sampling sites on the Lonar crater walls and the lake-bed was assessed using culture-independent molecular methods. Taxonomic classification of 16S rRNA gene sequences from all four basalt samples revealed similarities as well as dissimilarities in the presence or absence of several prokaryotic taxa. Cluster analysis of Denaturing gradient gel electrophoresis fingerprints and UniFrac analysis of clone library sequences suggested substantial variations in bacterial and archaeal diversity between crater-wall and lake-bed sites. Although sequences affiliated to the bacterial phyla <i>Actinobacteria</i>, <i>Acidobacteria</i> and <i>Chloroflexi</i> were relatively more abundant in crater-wall basalts than in lake-bed basalts; the reverse was observed for sequences related to <i>Proteobacteria</i>, <i>Firmicutes</i>, <i>Cyanobacteria</i> and <i>Bacteroidetes</i>. <i>Archaea</i> in crater-wall and lake-bed basalt libraries were almost completely represented by <i>Thaumarchaeota</i> and <i>Euryarchaeota</i>, respectively. Diversity indices and richness estimates suggested the diversity of endolithic <i>Bacteria</i> to be higher than that of <i>Archaea</i> in the Lonar crater basalts. A substantial number of clone library sequences did not affiliate with extant <i>Bacteria</i> and <i>Archaea</i>. The detection of several putative lineages associated with C, N and S cycling suggests that the Lonar crater basalts are colonized by metabolically diverse prokaryotic communities involved in biogeochemical cycling of major elements.
DOI: 10.6084/m9.figshare.1047263.v1
title: Molecular Characterization of Prokaryotic Communities Associated with Lonar Crater Basalts

description: The Lonar crater is an unusually well-preserved meteorite impact structure that is located in one of the largest volcanic provinces on Earth (i.e., the Deccan Traps in India). The diversity of endoliths in Lonar crater basalts or Deccan flood basalts is not known. Here, the phylogenetic diversity of endolithic <i>Bacteria</i> and <i>Archaea</i> inhabiting basalts retrieved from four discrete sampling sites on the Lonar crater walls and the lake-bed was assessed using culture-independent molecular methods. Taxonomic classification of 16S rRNA gene sequences from all four basalt samples revealed similarities as well as dissimilarities in the presence or absence of several prokaryotic taxa. Cluster analysis of Denaturing gradient gel electrophoresis fingerprints and UniFrac analysis of clone library sequences suggested substantial variations in bacterial and archaeal diversity between crater-wall and lake-bed sites. Although sequences affiliated to the bacterial phyla <i>Actinobacteria</i>, <i>Acidobacteria</i> and <i>Chloroflexi</i> were relatively more abundant in crater-wall basalts than in lake-bed basalts; the reverse was observed for sequences related to <i>Proteobacteria</i>, <i>Firmicutes</i>, <i>Cyanobacteria</i> and <i>Bacteroidetes</i>. <i>Archaea</i> in crater-wall and lake-bed basalt libraries were almost completely represented by <i>Thaumarchaeota</i> and <i>Euryarchaeota</i>, respectively. Diversity indices and richness estimates suggested the diversity of endolithic <i>Bacteria</i> to be higher than that of <i>Archaea</i> in the Lonar crater basalts. A substantial number of clone library sequences did not affiliate with extant <i>Bacteria</i> and <i>Archaea</i>. The detection of several putative lineages associated with C, N and S cycling suggests that the Lonar crater basalts are colonized by metabolically diverse prokaryotic communities involved in biogeochemical cycling of major elements.
DOI: 10.6084/m9.figshare.1047246
title: SMBE 2014 Posters

description: A set of 4 posters for SMBE 2014, all related to characterizing the effect of mutation and tRNA-mediated selection on codon-anticodon adaptation in bacteria and bacteriophages, together with a new Index of Translation Elongation that performs much better than CAI, tAI and other indices in predicting translation elongation efficiency.
DOI: 10.6084/m9.figshare.1047246.v1
title: SMBE 2014 Posters

description: A set of 4 posters for SMBE 2014, all related to characterizing the effect of mutation and tRNA-mediated selection on codon-anticodon adaptation in bacteria and bacteriophages, together with a new Index of Translation Elongation that performs much better than CAI, tAI and other indices in predicting translation elongation efficiency.
DOI: 10.6084/m9.figshare.1047244
title: Software DAMBE

description: Poster announcing a comprehensive software package for data analysis in molecular biology and evolution
DOI: 10.6084/m9.figshare.1047244.v1
title: Software DAMBE

description: Poster announcing a comprehensive software package for data analysis in molecular biology and evolution
DOI: 10.6084/m9.figshare.1047223
title: Justifying Patents: A Critique of the Deontological Approach

description: This thesis assesses philosophical arguments in favour of patent systems. These come in both consequentialist and deontological forms, the latter of which are the focus of this analysis. One kind of deontological argument is based on the concept of desert. I argue that on any plausible conception of desert, the patent system fails to distribute rewards as well as viable alternative systems could. The other kind of deontological argument claims that inventors are entitled to patent rights over their inventions as an extension of their natural rights, drawing on a Lockean account of the conditions of legitimate appropriation of unowned goods. After a discussion of the metaphysics of invention, and of the nature of the commons, I argue that Locke's conditions are not in fact always trivially satisfied in the case of patents. Furthermore, entitlement-based arguments conclude that because new inventions are unowned, claiming property rights in them involves only the same moral considerations that would apply in the state of nature. I argue that because we are not in the state of nature, pre-existing property rights also need to be taken into account, which conflict with patents. The broad conclusion of this thesis is that none of the plausible deontological arguments for patent systems are sound. The implication is that any justification of must therefore be made in consequentialist terms; this ultimately rests on strong empirical evidence rather than normative arguments alone.
DOI: 10.6084/m9.figshare.1047223.v1
title: Justifying Patents: A Critique of the Deontological Approach

description: This thesis assesses philosophical arguments in favour of patent systems. These come in both consequentialist and deontological forms, the latter of which are the focus of this analysis. One kind of deontological argument is based on the concept of desert. I argue that on any plausible conception of desert, the patent system fails to distribute rewards as well as viable alternative systems could. The other kind of deontological argument claims that inventors are entitled to patent rights over their inventions as an extension of their natural rights, drawing on a Lockean account of the conditions of legitimate appropriation of unowned goods. After a discussion of the metaphysics of invention, and of the nature of the commons, I argue that Locke's conditions are not in fact always trivially satisfied in the case of patents. Furthermore, entitlement-based arguments conclude that because new inventions are unowned, claiming property rights in them involves only the same moral considerations that would apply in the state of nature. I argue that because we are not in the state of nature, pre-existing property rights also need to be taken into account, which conflict with patents. The broad conclusion of this thesis is that none of the plausible deontological arguments for patent systems are sound. The implication is that any justification of must therefore be made in consequentialist terms; this ultimately rests on strong empirical evidence rather than normative arguments alone.