cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1320614
title: Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea Polynya, Antarctica

description: Phytoplankton blooms are an ecologically important yet not entirely understood phenomenon. This is certainly the case for the massive Phaeocystis blooms in climate-sensitive Antarctic polynyas. They interact with the atmosphere through the exchange of carbon dioxide and dimethylsulfide. They also sustain a distinct bacterial community that might play a role in bloom duration and intensity. Here we deeply sequenced a metagenome from an Amundsen Sea polynya bloom event and determined the genomic content of bacterial populations surrounding Phaeocystis. A pico-eukaryote genome (19.6 Mb) was also recovered. The identification of functional complementarities between P. antarctica and bacterial taxa organized in close association with Phaeocystis colonies makes a contribution to our understanding of bloom functioning in the Southern Ocean.
DOI: 10.6084/m9.figshare.1320613
title: SSW data and runscripts

description: Contains final SSW evolution data. Also includes runscripts and full run structure to re-create the full dataset, which can be expected to be about 2.2TB.
DOI: 10.6084/m9.figshare.1320632
title: Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics

description: Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for four months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n=2), Rhodanobacter (n=5), Acidobacteria (n=2), Sporolactobacillus (n=2, novel nitrogen fixing taxon), Ktedonobacter (n=1, second representative of the family Ktedonobacteraceae), Streptomyces (n=3, novel polyketide synthase modules) and Burkholderia (n=2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9Mb, with relative abundances ranging from rare (&lt;0.0001%) to relatively abundant (&gt;0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.
DOI: 10.6084/m9.figshare.1320632.v1
title: Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics

description: Despite extensive direct sequencing efforts and advanced analytical tools, reconstructing microbial genomes from soil using metagenomics have been challenging due to the tremendous diversity and relatively uniform distribution of genomes found in this system. Here we used enrichment techniques in an attempt to decrease the complexity of a soil microbiome prior to sequencing by submitting it to a range of physical and chemical stresses in 23 separate microcosms for four months. The metagenomic analysis of these microcosms at the end of the treatment yielded 540Mb of assembly using standard de novo assembly techniques (a total of 559,555 genes and 29,176 functions), from which we could recover novel bacterial genomes, plasmids and phages. The recovered genomes belonged to Leifsonia (n=2), Rhodanobacter (n=5), Acidobacteria (n=2), Sporolactobacillus (n=2, novel nitrogen fixing taxon), Ktedonobacter (n=1, second representative of the family Ktedonobacteraceae), Streptomyces (n=3, novel polyketide synthase modules) and Burkholderia (n=2, includes mega-plasmids conferring mercury resistance). Assembled genomes averaged to 5.9Mb, with relative abundances ranging from rare (&lt;0.0001%) to relatively abundant (&gt;0.01%) in the original soil microbiome. Furthermore, we detected them in samples collected from geographically distant locations, particularly more in temperate soils compared to samples originating from high-latitude soils and deserts. To the best of our knowledge, this study is the first successful attempt to assemble multiple bacterial genomes directly from a soil sample. Our findings demonstrate that developing pertinent enrichment conditions can stimulate environmental genomic discoveries that would have been impossible to achieve with canonical approaches that focus solely upon post-sequencing data treatment.
DOI: 10.6084/m9.figshare.1320660.v1
title: 7 February 2015 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1320591
title: API Usage Databases

description: This dataset has the database dumps of API usages of APIs such as Guice, Guava, Easymock, Spring and Hibernate.
DOI: 10.6084/m9.figshare.1320614.v1
title: Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea Polynya, Antarctica

description: Phytoplankton blooms are an ecologically important yet not entirely understood phenomenon. This is certainly the case for the massive Phaeocystis blooms in climate-sensitive Antarctic polynyas. They interact with the atmosphere through the exchange of carbon dioxide and dimethylsulfide. They also sustain a distinct bacterial community that might play a role in bloom duration and intensity. Here we deeply sequenced a metagenome from an Amundsen Sea polynya bloom event and determined the genomic content of bacterial populations surrounding Phaeocystis. A pico-eukaryote genome (19.6 Mb) was also recovered. The identification of functional complementarities between P. antarctica and bacterial taxa organized in close association with Phaeocystis colonies makes a contribution to our understanding of bloom functioning in the Southern Ocean.
DOI: 10.6084/m9.figshare.1320613.v2
title: SSW data and runscripts

description: Contains final SSW evolution data. Also includes runscripts and full run structure to re-create the full dataset, which can be expected to be about 2.2TB.
DOI: 10.6084/m9.figshare.1320613.v1
title: SSW data & runscripts

description: Contains final SSW evolution data. Also includes runscripts and full run structure to re-create the full dataset, which can be expected to be about 2.2TB.
DOI: 10.6084/m9.figshare.1320614.v2
title: Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea Polynya, Antarctica

description: Phytoplankton blooms are an ecologically important yet not entirely understood phenomenon. This is certainly the case for the massive Phaeocystis blooms in climate-sensitive Antarctic polynyas. They interact with the atmosphere through the exchange of carbon dioxide and dimethylsulfide. They also sustain a distinct bacterial community that might play a role in bloom duration and intensity. Here we deeply sequenced a metagenome from an Amundsen Sea polynya bloom event and determined the genomic content of bacterial populations surrounding Phaeocystis. A pico-eukaryote genome (19.6 Mb) was also recovered. The identification of functional complementarities between P. antarctica and bacterial taxa organized in close association with Phaeocystis colonies makes a contribution to our understanding of bloom functioning in the Southern Ocean.
DOI: 10.6084/m9.figshare.1320534
title: Raw Data (Tan et al. Variation in Burmese long-tailed macaque stone-tool use)

description: Tool use bouts coded from video data, and scan samples used for analyses in Tan et al. "Identifying variation in Burmese long-tailed macaque stone-tool use".
DOI: 10.6084/m9.figshare.1320614.v4
title: Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea Polynya, Antarctica

description: Phytoplankton blooms are an ecologically important yet not entirely understood phenomenon. This is certainly the case for the massive Phaeocystis blooms in climate-sensitive Antarctic polynyas. They interact with the atmosphere through the exchange of carbon dioxide and dimethylsulfide. They also sustain a distinct bacterial community that might play a role in bloom duration and intensity. Here we deeply sequenced a metagenome from an Amundsen Sea polynya bloom event and determined the genomic content of bacterial populations surrounding Phaeocystis. A pico-eukaryote genome (19.6 Mb) was also recovered. The identification of functional complementarities between P. antarctica and bacterial taxa organized in close association with Phaeocystis colonies makes a contribution to our understanding of bloom functioning in the Southern Ocean.
DOI: 10.6084/m9.figshare.1320660.v2
title: 7 February 2015 Field Notes

description: Field notes including image and/or video records. Original versions of all videos are available as of 20 Jan 2016 following the increase in allowed file size by figshare.
DOI: 10.6084/m9.figshare.1320591.v2
title: API Usage Databases

description: This dataset has the database dumps of API usages of APIs such as Guice, Guava, Spring and Hibernate.
DOI: 10.6084/m9.figshare.1320614.v3
title: Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea Polynya, Antarctica

description: Phytoplankton blooms are an ecologically important yet not entirely understood phenomenon. This is certainly the case for the massive Phaeocystis blooms in climate-sensitive Antarctic polynyas. They interact with the atmosphere through the exchange of carbon dioxide and dimethylsulfide. They also sustain a distinct bacterial community that might play a role in bloom duration and intensity. Here we deeply sequenced a metagenome from an Amundsen Sea polynya bloom event and determined the genomic content of bacterial populations surrounding Phaeocystis. A pico-eukaryote genome (19.6 Mb) was also recovered. The identification of functional complementarities between P. antarctica and bacterial taxa organized in close association with Phaeocystis colonies makes a contribution to our understanding of bloom functioning in the Southern Ocean.
DOI: 10.6084/m9.figshare.1320529
title: Dataset: Physical Intelligence Experiments

description: Referenced in: Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems, Nature Precedings, 2845.v1 (2009) and Performance augmentation in hybrid bionic systems: techniques and experiment, arXiv:0810.4629 (2008) and Naturally Supervised Learning in Manipulable Technologies, arXiv:1106.1105 (2011).
DOI: 10.6084/m9.figshare.1320528
title: Dataset: Fibroblast Reprogramming Diversity

description: Referenced in: "Defining phenotypic respecification diversity using multiple cell lines and reprogramming regimens". Stem Cells and Development, 22(19), 2641-2654 (2013) and "Cellular decision-making bias: the missing ingredient in cell functional diversity". arXiv:1310.8268 (2013).
DOI: 10.6084/m9.figshare.1320447
title: Gaussian Job Archive for FH13O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320450
title: Library survey - Staff 24/02/2015

description: Answers to questions on when and to what purposes INSA Rennes staff go to the libraries (70 respondents)
DOI: 10.6084/m9.figshare.1320591.v3
title: API Usage Databases

description: This dataset has the database dumps of API usages of APIs such as Guice, Guava, Spring and Hibernate.
DOI: 10.6084/m9.figshare.1320447.v1
title: Gaussian Job Archive for FH13O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320450.v1
title: Library survey - Staff 24/02/2015

description: Answers to questions on when and to what purposes INSA Rennes staff go to the libraries (70 respondents)
DOI: 10.6084/m9.figshare.1320389
title: Gaussian Job Archive for H7IO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320419
title: Gaussian Job Archive for H9IO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320591.v4
title: API Usage Databases

description: This dataset has the database dumps of API usages of APIs such as Guice, Guava, Spring and Hibernate.
DOI: 10.6084/m9.figshare.1320387
title: Gaussian Job Archive for H7IO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320388
title: Gaussian Job Archive for H9IO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320387.v1
title: Gaussian Job Archive for H7IO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320419.v1
title: Gaussian Job Archive for H9IO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320388.v1
title: Gaussian Job Archive for H9IO4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320384
title: Gaussian Job Archive for H3IO

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320385
title: Gaussian Job Archive for H5IO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320386
title: Gaussian Job Archive for H5IO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320591.v5
title: API Usage Databases

description: This dataset has the database dumps of API usages of APIs such as Guice, Guava, Spring and Hibernate.
DOI: 10.6084/m9.figshare.1320383
title: Gaussian Job Archive for H3IO

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320385.v1
title: Gaussian Job Archive for H5IO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320386.v1
title: Gaussian Job Archive for H5IO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320591.v6
title: API Usage Databases

description: This dataset has the database dumps of API usages of APIs such as Guice, Guava, Spring and Hibernate.
DOI: 10.6084/m9.figshare.1320382
title: All populations CNV Data

description: This dataset contains Copy Number Variation breakpoint data of YRI, CEU, Ashkenazi Jews I, Ashkenazi Jews II, China, Tibet, India, JPT, Australia, New World, and Taiwan populations.
DOI: 10.6084/m9.figshare.1320383.v1
title: Gaussian Job Archive for H3IO

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320384.v1
title: Gaussian Job Archive for H3IO

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319614
title: De-regulated expression of the BRG1 chromatin remodeling factor in bone marrow mesenchymal stromal cells induces senescence associated with the silencing of NANOG and changes in the levels of chromatin proteins

description: Stem cells have a peculiar chromatin architecture that contributes to their unique properties, including uncommitted status, multi/pluripotency and self-renewal. We analyzed the effect of the de-regulation of the SWI/SNF chromatin remodeling complex in mesenchymal stromal cells (MSC) through the silencing and up-regulation of BRG1, which is the ATPase subunit of the complex. The altered expression of BRG1 promoted the senescence of MSC with suppression of the NANOG transcription, which is part of the transcriptional circuitry governing stem cell functions. To gain insight on the way NANOG was silenced, we evaluated how the de-regulated BRG1 expression affect the binding of activators and repressors on the NANOG promoter. We found 4 E2F binding motifs on NANOG promoter, which can be occupied by RB1 and RB2/P130. These are members of the retinoblastoma gene family. In MSC with a silenced BRG1, the relative binding of the 2 retinoblastoma proteins increased, and this was associated with the recruitment of DNMT1. This induced the methylation of CpG on the NANOG promoter. Opposingly, when a high level of BRG1 was present, the same E2F binding motifs were docking sites for BRG1, which induced chromatin compaction without CpG methylation but with increased histone deacetylation, associated with the presence of HDAC1 on E2F binding sites. Besides the sharp regulation of the NANOG expression, we evidenced, through proteomic analysis, that the de-regulation of the SWI/SNF function affected the expression of histones and other nuclear proteins involved in “nuclear architecture,” suggesting that BRG1 may act as global regulator of gene expression.
DOI: 10.6084/m9.figshare.1320591.v7
title: API Usage Databases

description: This dataset has the database dumps of API usages of APIs such as Guice, Guava, Spring and Hibernate.
DOI: 10.6084/m9.figshare.1319611
title: Gaussian Job Archive for BrH11O5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319611.v1
title: Gaussian Job Archive for BrH11O5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1320382.v1
title: All populations CNV Data

description: This dataset contains Copy Number Variation breakpoint data of YRI, CEU, Ashkenazi Jews I, Ashkenazi Jews II, China, Tibet, India, JPT, Australia, New World, and Taiwan populations.
DOI: 10.6084/m9.figshare.1320591.v8
title: API Usage Databases

description: This dataset has the database dumps of API usages of APIs such as Guice, Guava, Easymock, Spring and Hibernate.
DOI: 10.6084/m9.figshare.1319608
title: Gaussian Job Archive for FH11O5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319587
title: Gaussian Job Archive for FH9O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319587.v1
title: Gaussian Job Archive for FH9O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319608.v1
title: Gaussian Job Archive for FH11O5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319614.v1
title: De-regulated expression of the BRG1 chromatin remodeling factor in bone marrow mesenchymal stromal cells induces senescence associated with the silencing of NANOG and changes in the levels of chromatin proteins

description: Stem cells have a peculiar chromatin architecture that contributes to their unique properties, including uncommitted status, multi/pluripotency and self-renewal. We analyzed the effect of the de-regulation of the SWI/SNF chromatin remodeling complex in mesenchymal stromal cells (MSC) through the silencing and up-regulation of BRG1, which is the ATPase subunit of the complex. The altered expression of BRG1 promoted the senescence of MSC with suppression of the NANOG transcription, which is part of the transcriptional circuitry governing stem cell functions. To gain insight on the way NANOG was silenced, we evaluated how the de-regulated BRG1 expression affect the binding of activators and repressors on the NANOG promoter. We found four E2F binding motifs on NANOG promoter, which can be occupied by RB1 and RB2/P130. These are members of the retinoblastoma gene family. In MSC with a silenced BRG1, the relative binding of the two retinoblastoma proteins increased, and this was associated with the recruitment of DNMT1. This induced the methylation of CpG on the NANOG promoter. Opposingly, when a high level of BRG1 was present, the same E2F binding motifs were docking sites for BRG1, which induced chromatin compaction without CpG methylation but with increased histone deacetylation, associated with the presence of HDAC1 on E2F binding sites.Besides the sharp regulation of the NANOG expression, we evidenced, through proteomic analysis, that the de-regulation of the SWI/SNF function affected the expression of histones and other nuclear proteins involved in “nuclear architecture,” suggesting that BRG1 may act as global regulator of gene expression.
DOI: 10.6084/m9.figshare.1319584
title: Gaussian Job Archive for BrH13O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319582
title: Data associated with the study entitled "Isolation by distance, not rivers, control the distribution of termite species in the Amazonian rain forest"

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319583
title: Gaussian Job Archive for BrH9O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319584.v1
title: Gaussian Job Archive for BrH13O6

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.