cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1598133
title: Genetic basis of natural variation in body pigmentation in <i>Drosophila melanogaster</i>

description: Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at <i>bab1, t</i> and <i>e</i> affect variation in abdominal pigmentation in several populations of <i>Drosophila melanogaster</i>. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the <i>Drosophila</i> Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in <i>bab1, t</i> and <i>e</i>; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including <i>bab1, t</i> and <i>e</i> and 7 genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of <i>Drosophila</i> pigmentation is complex, with a few major genes and many other loci with smaller effects.
DOI: 10.6084/m9.figshare.1598138.v1
title: Cannabis Liberalization and Adolescent Cannabis Use: A Cross-national Study in 38 Countries_Appendix

description: Supplementary tables for paper "Cannabis Liberalization and Adolescent Cannabis Use: A Cross-national Study in 38 Countries" by Shi. Y et al.
DOI: 10.6084/m9.figshare.1598122
title: Gaussian Job Archive for C6H15NO5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1598132
title: The Explorer Islamabad Issue 10

description: The Explorer Islamabad Issue 10
DOI: 10.6084/m9.figshare.1598132.v1
title: The Explorer Islamabad Issue 10

description: The Explorer Islamabad Issue 10
DOI: 10.6084/m9.figshare.1598122.v1
title: Gaussian Job Archive for C6H15NO5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1598133.v1
title: Genetic Basis of Natural Variation in Body Pigmentation in Drosophila melanogaster

description: Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at <i>bab1, t</i> and <i>e</i> affect variation in abdominal pigmentation in several populations of <i>Drosophila melanogaster</i>. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the <i>Drosophila</i> Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in <i>bab1, t</i> and <i>e</i>; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including <i>bab1, t</i> and <i>e</i> and seven genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of <i>Drosophila</i> pigmentation is complex, with a few major genes and many other loci with smaller effects.
DOI: 10.6084/m9.figshare.1598133.v3
title: Genetic basis of natural variation in body pigmentation in <i>Drosophila melanogaster</i>

description: Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at <i>bab1, t</i> and <i>e</i> affect variation in abdominal pigmentation in several populations of <i>Drosophila melanogaster</i>. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the <i>Drosophila</i> Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in <i>bab1, t</i> and <i>e</i>; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including <i>bab1, t</i> and <i>e</i> and 7 genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of <i>Drosophila</i> pigmentation is complex, with a few major genes and many other loci with smaller effects.
DOI: 10.6084/m9.figshare.1598133.v2
title: Genetic Basis of Natural Variation in Body Pigmentation in Drosophila melanogaster

description: Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at <i>bab1, t</i> and <i>e</i> affect variation in abdominal pigmentation in several populations of <i>Drosophila melanogaster</i>. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the <i>Drosophila</i> Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in <i>bab1, t</i> and <i>e</i>; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including <i>bab1, t</i> and <i>e</i> and seven genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of <i>Drosophila</i> pigmentation is complex, with a few major genes and many other loci with smaller effects.
DOI: 10.6084/m9.figshare.1598098
title: Raw data

description: Annotation and Functional Assessment of Transporters in Aspergillus oryzae Metabolism
DOI: 10.6084/m9.figshare.1598104
title: Motif analysis results

description: Files belonging to a manual analysis of motifs of workflows belonging to Wings, Taverna, Galaxy and VisTrails. More details on how these files were obtained can be seen in http://dx.doi.org/10.1016/j.future.2013.09.018 and http://purl.org/net/ro-motifPaper
DOI: 10.6084/m9.figshare.1598104.v1
title: Motif analysis results

description: Files belonging to a manual analysis of motifs of workflows belonging to Wings, Taverna, Galaxy and VisTrails. More details on how these files were obtained can be seen in http://dx.doi.org/10.1016/j.future.2013.09.018 and http://purl.org/net/ro-motifPaper
DOI: 10.6084/m9.figshare.1598097
title: result qtransporter_DB Hit db_A_oryzae

description: result qtransporter_DB Hit db_A_oryzae
DOI: 10.6084/m9.figshare.1598094
title: Gaussian Job Archive for C6H14O5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1598094.v1
title: Gaussian Job Archive for C6H14O5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1598098.v1
title: Raw data

description: Annotation and Functional Assessment of Transporters in Aspergillus oryzae Metabolism
DOI: 10.6084/m9.figshare.1598097.v1
title: result qtransporter_DB Hit db_A_oryzae

description: result qtransporter_DB Hit db_A_oryzae
DOI: 10.6084/m9.figshare.1598098.v3
title: Raw data

description: Annotation and Functional Assessment of Transporters in Aspergillus oryzae Metabolism
DOI: 10.6084/m9.figshare.1598097.v3
title: result qtransporter_DB Hit db_A_oryzae

description: result qtransporter_DB Hit db_A_oryzae
DOI: 10.6084/m9.figshare.1598098.v2
title: Raw data

description: Annotation and Functional Assessment of Transporters in Aspergillus oryzae Metabolism
DOI: 10.6084/m9.figshare.1598097.v2
title: result qtransporter_DB Hit db_A_oryzae

description: result qtransporter_DB Hit db_A_oryzae
DOI: 10.6084/m9.figshare.1598073
title: nations_capitols

description: Nation capitols
DOI: 10.6084/m9.figshare.1598072
title: siRNA sub-cellular localization-SI

description: Compressed files for densities for RNA strands, RISC molecules, and RISC-target complexes computed from Equ. (3) in paper entitled "Non-catalytic RISCs and kinetics determine mammalian siRNA sub-cellular localization", to be published in PLOS ONE, doi:10.1371/journal.pone.0143182. Initial condition and other details described in Methods section after Equ. (3). Values for reaction parameters given in Table 1.
DOI: 10.6084/m9.figshare.1598067
title: organisms.txt

description: organisms
DOI: 10.6084/m9.figshare.1598073.v1
title: nations_capitols

description: Nation capitols
DOI: 10.6084/m9.figshare.1598088.v1
title: Learning in MOOCS: A Comparison Study

description: Abstract for presentation at eMOOCS 2016. Full paper will be available in cofnerence proceedings.
DOI: 10.6084/m9.figshare.1598066
title: file1

description: file1
DOI: 10.6084/m9.figshare.1598064
title: file3

description: file3
DOI: 10.6084/m9.figshare.1598065
title: file2

description: file2
DOI: 10.6084/m9.figshare.1598061
title: Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird

description: This data has been used to publish the following paper in PLoS ONE: Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird The dataset contains 6 sheets cited in Table 1 (statistical analysis) of the article.
DOI: 10.6084/m9.figshare.1598064.v1
title: file3

description: file3
DOI: 10.6084/m9.figshare.1598065.v1
title: file2

description: file2
DOI: 10.6084/m9.figshare.1598072.v1
title: Non-catalytic RISCs and kinetics determine mammalian siRNA sub-cellular localization - Supplementary Information

description: Compressed files for densities for RNA strands, RISC molecules, and RISC-target complexes computed from Equ. (3) in paper given in Title. Initial condition and other details described in Methods section after Equ. (3). Values for reaction parameters given in Table 1.
DOI: 10.6084/m9.figshare.1598025
title: Gaussian Job Archive for C11H20N2O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1598061.v2
title: Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird

description: This data has been used to publish the following paper in PLoS ONE: Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird The dataset contains 6 sheets cited in Table 1 (statistical analysis) of the article.
DOI: 10.6084/m9.figshare.1598025.v1
title: Gaussian Job Archive for C11H20N2O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1598061.v1
title: Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird

description: This data has been used to publish the following paper in PLoS ONE: Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird The dataset contains 6 sheets cited in Table 1 (statistical analysis) of the article.
DOI: 10.6084/m9.figshare.1598072.v2
title: siRNA sub-cellular localization-SI

description: Compressed files for densities for RNA strands, RISC molecules, and RISC-target complexes computed from Equ. (3) in paper entitled "Non-catalytic RISCs and kinetics determine mammalian siRNA sub-cellular localization", to be published in PLOS ONE, doi:10.1371/journal.pone.0143182. Initial condition and other details described in Methods section after Equ. (3). Values for reaction parameters given in Table 1.
DOI: 10.6084/m9.figshare.1598072.v4
title: siRNA sub-cellular localization-SI

description: Compressed files for densities for RNA strands, RISC molecules, and RISC-target complexes computed from Equ. (3) in paper entitled "Non-catalytic RISCs and kinetics determine mammalian siRNA sub-cellular localization", to be published in PLOS ONE, doi:10.1371/journal.pone.0143182. Initial condition and other details described in Methods section after Equ. (3). Values for reaction parameters given in Table 1.
DOI: 10.6084/m9.figshare.1598012
title: Gaussian Job Archive for C11H21ClN2O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1598012.v1
title: Gaussian Job Archive for C11H21ClN2O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1598072.v3
title: siRNA sub-cellular localization-SI

description: Compressed files for densities for RNA strands, RISC molecules, and RISC-target complexes computed from Equ. (3) in paper entitled "Non-catalytic RISCs and kinetics determine mammalian siRNA sub-cellular localization", to be published in PLOS ONE, doi:10.1371/journal.pone.0143182. Initial condition and other details described in Methods section after Equ. (3). Values for reaction parameters given in Table 1.
DOI: 10.6084/m9.figshare.1598000
title: Specification Test for Spatial Autoregressive Models

description: This article considers a simple test for the correct specification of linear spatial autoregressive models, assuming that the choice of the weight matrix <i>W<sub>n</sub></i> is true. We derive the limiting distributions of the test under the null hypothesis of correct specification and a sequence of local alternatives. We show that the test is free of nuisance parameters asymptotically under the null and prove the consistency of our test. To improve the finite sample performance of our test, we also propose a residual-based wild bootstrap and justify its asymptotic validity. We conduct a small set of Monte Carlo simulations to investigate the finite sample properties of our tests. Finally, we apply the test to two empirical datasets: the vote cast and the economic growth rate. We reject the linear spatial autoregressive model in the vote cast example but fail to reject it in the economic growth rate example. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1598000.v2
title: Specification Test for Spatial Autoregressive Models

description: This article considers a simple test for the correct specification of linear spatial autoregressive models, assuming that the choice of the weight matrix <i>W<sub>n</sub></i> is true. We derive the limiting distributions of the test under the null hypothesis of correct specification and a sequence of local alternatives. We show that the test is free of nuisance parameters asymptotically under the null and prove the consistency of our test. To improve the finite sample performance of our test, we also propose a residual-based wild bootstrap and justify its asymptotic validity. We conduct a small set of Monte Carlo simulations to investigate the finite sample properties of our tests. Finally, we apply the test to two empirical datasets: the vote cast and the economic growth rate. We reject the linear spatial autoregressive model in the vote cast example but fail to reject it in the economic growth rate example. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1598001
title: Lipopolysaccharides may aggravate apoptosis through accumulation of autophagosomes in alveolar macrophages of human silicosis

description: Silica dust mainly attacks alveolar macrophages (AMs) and increases the apoptosis of AMs in silicosis patients. However, it is still unclear whether autophagy is affected. Autophagy mainly has defensive functions in response to stress, contributing to cell survival in adverse conditions, and conversely it has also been implicated in cell death. Lipopolysaccharide (LPS) induces autophagy and apoptosis in macrophages. The role of LPS in autophagy and apoptosis in AMs of silicosis patients is unknown. In this study, we collected AMs from 53 male workers exposed to silica and divided them into an observer (control) group, and stage I, II and III patient groups. We found increased levels of LC3B, SQSTM1/p62 and BECN1，whereas the phosphorylation of MTOR，and levels of LAMP2, TLR4, MYD88, TICAM1, as well as the number of lysosomes decreased with the development of silicosis. LPS stimulation triggered autophagy and increased levels of SQSTM1 in AMs. The autophagy inhibitor, 3-methyladenine (3MA), inhibited LPS-induced apoptosis in the AMs of silicosis patients. Moreover, 3MA reversed the LPS-induced decrease in BCL2 and the increase in BAX and CASP3 levels in AMs. These results suggest that autophagosomes accumulate in AMs during silicosis progression. LPS can induce the formation of autophagosomes through a TLR4-dependent pathway, and LPS may exacerbate the apoptosis in AMs. Blockade of the formation of autophagosomes may inhibit LPS-induced apoptosis via the intrinsic apoptotic pathway in AMs. These findings describe novel mechanisms that may lead to new preventive and therapeutic strategies for pulmonary fibrosis.
DOI: 10.6084/m9.figshare.1598001.v2
title: Lipopolysaccharides may aggravate apoptosis through accumulation of autophagosomes in alveolar macrophages of human silicosis

description: Silica dust mainly attacks alveolar macrophages (AMs) and increases the apoptosis of AMs in silicosis patients. However, it is still unclear whether autophagy is affected. Autophagy mainly has defensive functions in response to stress, contributing to cell survival in adverse conditions, and conversely it has also been implicated in cell death. Lipopolysaccharide (LPS) induces autophagy and apoptosis in macrophages. The role of LPS in autophagy and apoptosis in AMs of silicosis patients is unknown. In this study, we collected AMs from 53 male workers exposed to silica and divided them into an observer (control) group, and stage I, II and III patient groups. We found increased levels of LC3B, SQSTM1/p62 and BECN1，whereas the phosphorylation of MTOR，and levels of LAMP2, TLR4, MYD88, TICAM1, as well as the number of lysosomes decreased with the development of silicosis. LPS stimulation triggered autophagy and increased levels of SQSTM1 in AMs. The autophagy inhibitor, 3-methyladenine (3MA), inhibited LPS-induced apoptosis in the AMs of silicosis patients. Moreover, 3MA reversed the LPS-induced decrease in BCL2 and the increase in BAX and CASP3 levels in AMs. These results suggest that autophagosomes accumulate in AMs during silicosis progression. LPS can induce the formation of autophagosomes through a TLR4-dependent pathway, and LPS may exacerbate the apoptosis in AMs. Blockade of the formation of autophagosomes may inhibit LPS-induced apoptosis via the intrinsic apoptotic pathway in AMs. These findings describe novel mechanisms that may lead to new preventive and therapeutic strategies for pulmonary fibrosis.
DOI: 10.6084/m9.figshare.1598000.v1
title: Specification Test for Spatial Autoregressive Models

description: This paper considers a simple test for the correct specification of linear spatial autoregressive models, assuming that the choice of the weight matrix <i>W</i><sub><i>n</i></sub> is true. We derive the limiting distributions of the test under the null hypothesis of correct specification and a sequence of local alternatives. We show that the test is free of nuisance parameters asymptotically under the null and prove the consistency of our test. To improve the finite sample performance of our test, we also propose a residual-based wild bootstrap and justify its asymptotic validity. We conduct a small set of Monte Carlo simulations to investigate the finite sample properties of our tests. Finally, we apply the test to two empirical datasets: the vote cast and the economic growth rate. We reject the linear spatial autoregressive model in the vote cast example but fail to reject it in the economic growth rate example.
DOI: 10.6084/m9.figshare.1597995
title: Pegasus Basin, eastern New Zealand: A stratigraphic record of subsidence and subduction, ancient and modern

description: The stratigraphic architecture of a thick (c. 9000 m) Albian–Recent sedimentary succession within the Pegasus Basin is presented here, based primarily on interpretation of the New Zealand Government's ‘PEG09’ 2D reconnaissance seismic survey. The basin lies immediately east and outboard of the Hikurangi subduction zone, and formed mainly because of Neogene downwarping of the underlying Pacific Plate near the transition from subduction to oblique-slip faulting. The basin fill is little deformed by the Neogene–Recent convergent margin tectonics that pervasively deform the adjacent East Coast Basin. Four large-scale tectonostratigraphic units are differentiated: (1) metasedimentary ‘basement’ rocks, deposited and accreted within the Gondwana Mesozoic accretionary wedge; (2) Early Cretaceous Large Igneous Province crust of the Hikurangi Plateau; (3) non-accreted ‘cover’ strata, incorporating rocks age-equivalent to the youngest parts of the Gondwana accretionary wedge, plus the overlying Late Cretaceous and Paleogene rocks deposited during thermal subsidence; and (4) Neogene–Recent strata deposited since the renewal of subduction beneath eastern North Island. The pre-Neogene geology illustrated by the seismic data describes the Mesozoic subduction along the Gondwana margin, ‘frozen’ at the time when active subduction accretion ceased at c. 110–105 Ma. The geology of Pegasus Basin also provides an insight into the much-debated relationship between ‘basement’ and ‘cover’ rocks in the East Coast Basin. This study is also relevant to the assessment of the petroleum potential of the basin, which is currently held under licence.