cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.157207.v1
title: Figure 4 raw data

description: Fluorescence levels of Iba1 and cd11b at three days post chorda tympani transection (CTx) in animals that were treated with minocycline (Mino) and animals that were not treated (No Mino). Three animals for each treatment, Mino and No Mino, were analyzed. The fluorescent intensity of Iba1 and cd11b were measured within a defined circular region of interest (ROI=1,596 40 µm2) in ImageJ. For each animal, two ROI measurements were taken at levels R2 (sheet 1) and R3 (sheet 2) on the intact (Int) and transected (Tx) sides in the following regions: rostral central (RC) subnucleus of the nTS, ventral (V) subnucleus of the nTS and the spinal vestibular nucleus (SpVe). The fluorescent levels on the transected sides were normalized by subtracting the fluorescent levels from the intact sides. These normalized values, which were used to generate the graphs shown in Figure 4, were then analyzed using SPSS software with the appropriate 2-way ANOVAs and Tukey’s post-hoc analysis where significant differences were defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157206.v2
title: Number of microglia in the nTS three days post chorda tympani transection in mice treated with minocycline, saline or no treatment

description: The number of microglia in the rostral central (RC) subnucleus of the nTS at three days post chorda tympani transection (CTx) in mice treated with minocycline (Mino), saline or no treatment. Three animals from each treatment were analyzed. From each animal, six microglial counts were taken throughout the rostral levels on both intact (Int) and transected (Tx) sides. The cell counts were analyzed using SPSS software with appropriate ANOVAs and Tukey’s post-hoc analysis. Significance was defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157206.v1
title: Figure 3 raw data

description: The number of microglia in the rostral central (RC) subnucleus of the nTS at three days post chorda tympani transection (CTx) in mice treated with minocycline (Mino), saline or no treatment. Three animals from each treatment were analyzed. From each animal, six microglial counts were taken throughout the rostral levels on both intact (Int) and transected (Tx) sides. The cell counts were analyzed using SPSS software with appropriate ANOVAs and Tukey’s post-hoc analysis. Significance was defined as p&lt;0.05.
DOI: 10.6084/m9.figshare.157197
title: air_metadata.txt

description: Airborne bacterial 16S sequence metadata from university classroom building
DOI: 10.6084/m9.figshare.157199
title: airborne sequence data

description: Sequence file has been compliled from multiple partial MiSeq runs, thus multiple barcodes were reused. The sequence file contains identifiers where barcoded sequences have already been binned into individual samples. Sample names correspond to the sample.id column in the metadata file. UPDATE: This study was published in Indoor Air: Meadow JF, Altrichter AE, Kembel SW, Kline J, Mhuireach G, Moriyama M, Northcutt D, O’Connor TK, Womack a M, Brown GZ, Green JL, Bohannan BJM: Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source. Indoor Air. 2013, 24:41–48.
DOI: 10.6084/m9.figshare.157198
title: Airborne bacterial 16S sequence data from university classroom building

description: Airborne bacterial 16S sequence data from university classroom building
DOI: 10.6084/m9.figshare.157199.v1
title: airborne sequence data

description: Sequence file has been compliled from multiple partial MiSeq runs, thus multiple barcodes were reused. The sequence file contains identifiers where barcoded sequences have already been binned into individual samples. Sample names correspond to the sample.id column in the metadata file. UPDATE: This study was published in Indoor Air: Meadow JF, Altrichter AE, Kembel SW, Kline J, Mhuireach G, Moriyama M, Northcutt D, O’Connor TK, Womack a M, Brown GZ, Green JL, Bohannan BJM: Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source. Indoor Air. 2013, 24:41–48.
DOI: 10.6084/m9.figshare.157197.v1
title: air_metadata.txt

description: Airborne bacterial 16S sequence metadata from university classroom building
DOI: 10.6084/m9.figshare.157198.v1
title: Airborne bacterial 16S sequence data from university classroom building

description: Airborne bacterial 16S sequence data from university classroom building
DOI: 10.6084/m9.figshare.157191
title: Raw reads from Kocuria sp. str. UCD-OTCP genome sequencing project

description: Raw paired-end 160bp Illumina MiSeq reads from genomic sequencing of Kocuria sp. str. UCD-OTCP
DOI: 10.6084/m9.figshare.157179
title: Raw Illumina reads from genomic sequencing of Microbacterium sp. str. UCD-TDU

description: Raw paired-end 160bp Illumina MiSeq reads from genomic sequencing of Microbacterium sp. str. UCD-TDU
DOI: 10.6084/m9.figshare.157190
title: Eisen et al. 1995. SNF2 Evolution datasets.

description: Sequence alignments and other information from Eisen et al. 1995. Nucleic Acids Res. 1995 Jul 25;23(14):2715-23.Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Eisen JA, Sweder KS, Hanawalt PC.
DOI: 10.6084/m9.figshare.157190.v1
title: Eisen et al. 1995. SNF2 Evolution datasets.

description: Sequence alignments and other information from Eisen et al. 1995. Nucleic Acids Res. 1995 Jul 25;23(14):2715-23.Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Eisen JA, Sweder KS, Hanawalt PC.
DOI: 10.6084/m9.figshare.157177
title: Gaussian Job Archive for C8H19ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.157178
title: Raw reads from genomic sequencing of Brachybacterium muris UCD-AY4

description: Raw Illumina MiSeq paired-end 160 bp reads from genomic sequencing of Brachybacterium muris UCD-AY4
DOI: 10.6084/m9.figshare.157177.v1
title: Gaussian Job Archive for C8H19ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.157179.v2
title: Raw Illumina reads from genomic sequencing of Microbacterium sp. str. UCD-TDU

description: Raw paired-end 160bp Illumina MiSeq reads from genomic sequencing of Microbacterium sp. str. UCD-TDU
DOI: 10.6084/m9.figshare.157175
title: Gaussian Job Archive for C8H19ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.157176
title: Gaussian Job Archive for C8H19ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.157179.v1
title: Raw Illumina reads for Microbacterium sp. str. UCD-TDU

description: Raw paired-end 160bp Illumina MiSeq reads from genomic sequencing of Microbacterium sp. str. UCD-TDU
DOI: 10.6084/m9.figshare.157175.v1
title: Gaussian Job Archive for C8H19ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.157176.v1
title: Gaussian Job Archive for C8H19ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.157178.v1
title: Raw reads from genomic sequencing of Brachybacterium muris UCD-AY4

description: Raw Illumina MiSeq paired-end 160 bp reads from genomic sequencing of Brachybacterium muris UCD-AY4
DOI: 10.6084/m9.figshare.157178.v2
title: Raw reads from genomic sequencing of Brachybacterium muris UCD-AY4. http://dx.doi.org/10.6084/m9.figshare.157178

description: Raw Illumina MiSeq paired-end 160 bp reads from genomic sequencing of Brachybacterium muris UCD-AY4
DOI: 10.6084/m9.figshare.157178.v3
title: Raw reads from genomic sequencing of Brachybacterium muris UCD-AY4

description: Raw Illumina MiSeq paired-end 160 bp reads from genomic sequencing of Brachybacterium muris UCD-AY4
DOI: 10.6084/m9.figshare.157168
title: Synthesis of Cylindricine derivative

description: This is a synthesis of a cylindricine derivative. The 14th step is a cyclization and has been omitted due to the fact that the particular reaction has not yet been published. However, any suitable cyclization could be used at this step. This synthesis was made slightly longer to allow for the incorporation of the specialized reaction. However, some might find the other synthetic transformations interesting/useful for similar structures. The synthesis of the SM has now also been added..
DOI: 10.6084/m9.figshare.157173.v1
title: Synthesis of Fluroene Derivatives

description: Methods to acces various Fluroene derivatives.
DOI: 10.6084/m9.figshare.157113
title: INSTRUCTIONAL GARDEN: AN INSTRUMENT TO ENHANCE STUDENTS ACADEMIC PERFORMANCE

description: Aligned with the vision of achieving school mission on academic competence, this action research was conceived. This involves the integration of the beautification and the academic endeavour of all the subjects. The competencies/concepts for a corresponding grading period and subject are placed artistically in each garden. The UbD way that includes the stages: explore, firm-up, deepen and transfer are in evident in the gardens. The whole school Approach is employed in this endeavour with the stakeholders giving commitment. Students, teachers and the stakeholders work together in making their respective gardens beautiful and substantial.
DOI: 10.6084/m9.figshare.157165
title: 2013 Identity Awareness of Research Data

description: Four (4) images identity of research data where data is at the core of publication consideration.
DOI: 10.6084/m9.figshare.157168.v1
title: Synthesis of Cylindracine derivative

description: This is a synthesis of a cylindracine derivative. The 14th step is a cyclization and has been omitted due to the fact that the particular reaction has not yet been published. However, any suitable cyclization could be used at this step. This synthesis was made slightly longer to allow for the incorporation of the specialized reaction. However, some might find the other synthetic transformations interesting/useful for similar structures.
DOI: 10.6084/m9.figshare.157113.v1
title: INSTRUCTIONAL GARDEN: AN INSTRUMENT TO ENHANCE STUDENTS ACADEMIC PERFORMANCE

description: Aligned with the vision of achieving school mission on academic competence, this action research was conceived. This involves the integration of the beautification and the academic endeavour of all the subjects. The competencies/concepts for a corresponding grading period and subject are placed artistically in each garden. The UbD way that includes the stages: explore, firm-up, deepen and transfer are in evident in the gardens. The whole school Approach is employed in this endeavour with the stakeholders giving commitment. Students, teachers and the stakeholders work together in making their respective gardens beautiful and substantial.
DOI: 10.6084/m9.figshare.157168.v2
title: Synthesis of Cylindracine derivative

description: This is a synthesis of a cylindracine derivative. The 10th step is a cyclization and has been omitted due to the fact that the particular reaction has not yet been published. However, any suitable cyclization could be used at this step. This synthesis was made slightly longer to allow for the incorporation of the specialized reaction. However, some might find the other synthetic transformations interesting/useful for similar structures. My apologies: (previously the wrong figure was attacthed).
DOI: 10.6084/m9.figshare.157168.v3
title: Synthesis of Cylindracine derivative

description: This is a synthesis of a cylindracine derivative. The 14th step is a cyclization and has been omitted due to the fact that the particular reaction has not yet been published. However, any suitable cyclization could be used at this step. This synthesis was made slightly longer to allow for the incorporation of the specialized reaction. However, some might find the other synthetic transformations interesting/useful for similar structures. My apologies: (previously the wrong figure was attacthed).
DOI: 10.6084/m9.figshare.157107
title: GenoCAD Legacy Grammars

description: This fileset includes three grammars that were described in papers related to GenoCAD published between 2007 and 2010. These grammars can be imported into GenoCAD.
DOI: 10.6084/m9.figshare.157107.v2
title: GenoCAD Legacy Grammars

description: This fileset includes three grammars that were described in papers related to GenoCAD published between 2007 and 2010. These grammars can be imported into GenoCAD.
DOI: 10.6084/m9.figshare.157168.v4
title: Synthesis of Cylindracine derivative

description: This is a synthesis of a cylindracine derivative. The 14th step is a cyclization and has been omitted due to the fact that the particular reaction has not yet been published. However, any suitable cyclization could be used at this step. This synthesis was made slightly longer to allow for the incorporation of the specialized reaction. However, some might find the other synthetic transformations interesting/useful for similar structures. In figure 2 the 10th step is omitted, it was a cyclization, but there were problems with this synthetic method. My apologies: (previously the wrong figure was attacthed) but I've decided to keep both up to avoid confusion. :)
DOI: 10.6084/m9.figshare.157107.v1
title: GenoCAD Legacy Grammars

description: This fileset includes three grammars that were described in papers related to GenoCAD published between 2007 and 2010. These grammars can be imported into GenoCAD.
DOI: 10.6084/m9.figshare.157109.v2
title: Vessel Archives: A Strategic Approach to Existential Risk, Human Survival, and the Future of Life in the Universe (Preprint submission version)

description: Preprint submission version of paper for the 100 Year Starship Symposium Proceedings (2012): <em><strong>Vessel Archives: A Strategic Approach to Existential Risk, Human Survival, and the Future of Life in the Universe.</strong></em> <strong>Abstract:</strong> The abundance of ancient worlds detected by the Kepler Mission and others brings the persistence of the Fermi Paradox into stark relief. If an existential (sterilizing) risk to Earth emerged before an interstellar civilization were established, it could eliminate the prospects for complex life across an unknowable span of future time. In the absence of evidence of interstellar life, we must cultivate life on Earth as if the future of life in our region of the universe depended on it. Near-term, humanity must rise to its potential. Long-term, life must find a way. In this paper, we will propose an open project to collaboratively plan and build what we call Vessel Archives: Compact, focused habitats that foster our most sustainable methods and our most aspirational traces during our immediate challenges, emphasizing 100 Year Starship efforts as a milestone on our journey. Yet Vessel Archives would also serve as long-term cultural, biological, and geological archives within self-sustaining biospheres. We explore definitions and classifications of existential risk; the roots of Vessel Archives in architecture and archival; using the techniques of synthetic biology to encode digital data in DNA; tension between curation and sampling through the lens of Benford’s “Library of Life” proposal; and the aspiration that Vessel Archives serve as galvanizing beacons for humanity. <strong>Keywords:</strong> Existential Risk Archival Biophilic Design Pattern Language Arcology Synthetic Biology
DOI: 10.6084/m9.figshare.157109.v1
title: Vessel Archives: A Strategic Approach to Existential Risk, Human Survival, and the Future of Life in the Universe

description: Preprint submission version of paper for the 100 Year Starship Symposium Proceedings (2012): <em><strong>Vessel Archives: A Strategic Approach to Existential Risk, Human Survival, and the Future of Life in the Universe.</strong></em> <strong>Abstract:</strong> The abundance of ancient worlds detected by the Kepler Mission and others brings the persistence of the Fermi Paradox into stark relief. If an existential (sterilizing) risk to Earth emerged before an interstellar civilization were established, it could eliminate the prospects for complex life across an unknowable span of future time. In the absence of evidence of interstellar life, we must cultivate life on Earth as if the future of life in our region of the universe depended on it. Near-term, humanity must rise to its potential. Long-term, life must find a way. In this paper, we will propose an open project to collaboratively plan and build what we call Vessel Archives: Compact, focused habitats that foster our most sustainable methods and our most aspirational traces during our immediate challenges, emphasizing 100 Year Starship efforts as a milestone on our journey. Yet Vessel Archives would also serve as long-term cultural, biological, and geological archives within self-sustaining biospheres. We explore definitions and classifications of existential risk; the roots of Vessel Archives in architecture and archival; using the techniques of synthetic biology to encode digital data in DNA; tension between curation and sampling through the lens of Benford’s “Library of Life” proposal; and the aspiration that Vessel Archives serve as galvanizing beacons for humanity. <strong>Keywords:</strong> Existential Risk Archival Biophilic Design Pattern Language Arcology Synthetic Biology
DOI: 10.6084/m9.figshare.157168.v5
title: Synthesis of Cylindracine derivative

description: This is a synthesis of a cylindracine derivative. The 14th step is a cyclization and has been omitted due to the fact that the particular reaction has not yet been published. However, any suitable cyclization could be used at this step. This synthesis was made slightly longer to allow for the incorporation of the specialized reaction. However, some might find the other synthetic transformations interesting/useful for similar structures. The synthesis of the SM has now also been added.
DOI: 10.6084/m9.figshare.157104.v1
title: Baird-Rezabek Tri-Hex Vessel Fractal - CC BY-SA 3.0 2012

description: This fractal was calculated by mathematician Eric Baird, based on descriptions by myself, for us as a design template and prototype for physical structures described in my paper, <strong>Vessel Archives: A Strategic Approach to Existential Risk, Human Survival, and the Future of Life in the Universe.</strong>
DOI: 10.6084/m9.figshare.157168.v7
title: Synthesis of Cylindricine derivative

description: This is a synthesis of a cylindricine derivative. The 14th step is a cyclization and has been omitted due to the fact that the particular reaction has not yet been published. However, any suitable cyclization could be used at this step. This synthesis was made slightly longer to allow for the incorporation of the specialized reaction. However, some might find the other synthetic transformations interesting/useful for similar structures. The synthesis of the SM has now also been added..
DOI: 10.6084/m9.figshare.157093
title: Gaussian Job Archive for C7H17ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.157168.v6
title: Synthesis of Cylindricine derivative

description: This is a synthesis of a cylindricine derivative. The 14th step is a cyclization and has been omitted due to the fact that the particular reaction has not yet been published. However, any suitable cyclization could be used at this step. This synthesis was made slightly longer to allow for the incorporation of the specialized reaction. However, some might find the other synthetic transformations interesting/useful for similar structures. The synthesis of the SM has now also been added..
DOI: 10.6084/m9.figshare.157093.v1
title: Gaussian Job Archive for C7H17ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.157104.v2
title: Baird-Rezabek Hri-hex Fractal - CC BY-SA 3.0 2012

description: This fractal was calculated by mathematician Eric Baird, based on descriptions by myself, for us as a design template and prototype for physical structures described in my paper, <strong>Vessel Archives: A Strategic Approach to Existential Risk, Human Survival, and the Future of Earth-Originating Life.</strong>
DOI: 10.6084/m9.figshare.157089
title: Syntax highlighting for LaTeX: minted

description: ...in which I demonstrate the minted package for LaTeX...
DOI: 10.6084/m9.figshare.157094.v1
title: Using the Past to Predict the Future: The Public Land Survey, 19th Century Climate and the PalEON Project

description: Presentation for the Yi-Fu Seminar at the University of Wisconsin-Madison's Department of Geography. Presented on February 15th by Simon Goring. The talk abstract is here: <strong>Using Historical Records to Help Predict the Future: The Public Land Survey, 19th Century Climate and the PalEON Project</strong> <em>Predicting the response of organisms to changing climates in the 21st century is a major conservation challenge. Standard practice uses the relationship between modern species ranges and climate to predict future distributions under various future climate scenarios. The widespread and significant land use conversion in North America, particularly in the upper Midwest, challenges the basic assumptions of this model. I use historical records of vegetation and climate to build a better understanding of the state of forests in the upper Midwest prior to European settlement. Pre-settlement forests show significantly different structure and composition than modern forests, and our interpretations of the kinds of climates that tree species can occupy is likely to be affected by the broad-scale changes brought about by agricultural conversion. This analysis forms part of the broader PalEON project, and I will highlight how the information we gain from historical data can inform and improve our estimates of future climate change, species distributions and, ultimately help inform conservation planning in the 21st century.</em>
DOI: 10.6084/m9.figshare.157085
title: GFF3 syntax highlighting for nano

description: ...in which I describe how to enable syntax highlighting for GFF3 with the nano text editor...
DOI: 10.6084/m9.figshare.157089.v1
title: Syntax highlighting for LaTeX: minted

description: ...in which I demonstrate the minted package for LaTeX...
DOI: 10.6084/m9.figshare.157079
title: Raw data for figure 1 and figure 2

description: Raw data tables showing the number of female wasps that landed on each plant with the different blends (A,B or C).
DOI: 10.6084/m9.figshare.157085.v1
title: GFF3 syntax highlighting for nano

description: ...in which I describe how to enable syntax highlighting for GFF3 with the nano text editor...
DOI: 10.6084/m9.figshare.157075
title: Gaussian Job Archive for C7H17ClO3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.157078
title: An Assessment of the Relevance of Parameters Used for Ground Motion Frequency Content Characterization with Application to Vrancea Subcrustal Earthquakes

description: Presentation at the 15th World Conference on Earthquake Engineering, Lisbon, Portugal, Sept. 24-28, 2012
DOI: 10.6084/m9.figshare.157078.v1
title: An Assessment of the Relevance of Parameters Used for Ground Motion Frequency Content Characterization with Application to Vrancea Subcrustal Earthquakes

description: Presentation at the 15th World Conference on Earthquake Engineering, Lisbon, Portugal, Sept. 24-28, 2012
DOI: 10.6084/m9.figshare.157075.v1
title: Gaussian Job Archive for C7H17ClO3

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