cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6807191.v1
title: CRISPR-Cas Systems in Multicellular Cyanobacteria

description: Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor &gt;40 different putative CRISPR repeat-spacer cassettes, while the number of <i>cas</i> gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria. The number of 1328 repeat-spacer arrays exceeded the total of 391 encoded Cas1 proteins suggesting a tendency for fragmentation or the involvement of alternative adaptation factors. The model cyanobacterium <i>Anabaena</i> sp. PCC 7120 contains only three <i>cas1</i> genes but hosts at least three Class 1, one Class 2 and five orphan repeat-spacer arrays, all of which exhibit crRNA-typical expression patterns suggesting active transcription, maturation and incorporation into CRISPR complexes. The CRISPR-Cas system within the element interrupting the <i>Anabaena</i> sp. PCC 7120 <i>fdxN</i> gene, as well as analogous arrangements in other strains, occupy the genetic elements that become excised during the differentiation-related programmed site-specific recombination. This fact indicates the propensity of these elements for the integration of CRISPR-<i>cas</i> systems and points to a previously not recognized connection. The possible Class 2 effector protein gene <i>all3613</i> is linked to a short repeat-spacer array and a single tRNA gene, similar to its homologs in other cyanobacteria. The diversity, high number and presence of CRISPR-Cas systems in DNA elements that are programmed for homologous recombination make filamentous cyanobacteria a prolific resource for their study.
DOI: 10.6084/m9.figshare.6807191.v3
title: CRISPR-Cas systems in multicellular cyanobacteria

description: Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor &gt; 40 different putative CRISPR repeat-spacer cassettes, while the number of <i>cas</i> gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria. The number of 1328 repeat-spacer arrays exceeded the total of 391 encoded Cas1 proteins suggesting a tendency for fragmentation or the involvement of alternative adaptation factors. The model cyanobacterium <i>Anabaena</i> sp. PCC 7120 contains only three <i>cas1</i> genes but hosts three Class 1, possibly one Class 2 and five orphan repeat-spacer arrays, all of which exhibit crRNA-typical expression patterns suggesting active transcription, maturation and incorporation into CRISPR complexes. The CRISPR-Cas system within the element interrupting the <i>Anabaena</i> sp. PCC 7120 <i>fdxN</i> gene, as well as analogous arrangements in other strains, occupy the genetic elements that become excised during the differentiation-related programmed site-specific recombination. This fact indicates the propensity of these elements for the integration of CRISPR-<i>cas</i> systems and points to a previously not recognized connection. The gene <i>all3613</i> resembling a possible Class 2 effector protein is linked to a short repeat-spacer array and a single tRNA gene, similar to its homologs in other cyanobacteria. The diversity and presence of numerous CRISPR-Cas systems in DNA elements that are programmed for homologous recombination make filamentous cyanobacteria a prolific resource for their study. <b>Abbreviations</b>: Cas: CRISPR associated sequences; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; C2c: Class 2 candidate; SDR: small dispersed repeat; TSS: transcriptional start site; UTR: untranslated region.
DOI: 10.6084/m9.figshare.6807191.v2
title: CRISPR-Cas systems in multicellular cyanobacteria

description: Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor &gt; 40 different putative CRISPR repeat-spacer cassettes, while the number of <i>cas</i> gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria. The number of 1328 repeat-spacer arrays exceeded the total of 391 encoded Cas1 proteins suggesting a tendency for fragmentation or the involvement of alternative adaptation factors. The model cyanobacterium <i>Anabaena</i> sp. PCC 7120 contains only three <i>cas1</i> genes but hosts three Class 1, possibly one Class 2 and five orphan repeat-spacer arrays, all of which exhibit crRNA-typical expression patterns suggesting active transcription, maturation and incorporation into CRISPR complexes. The CRISPR-Cas system within the element interrupting the <i>Anabaena</i> sp. PCC 7120 <i>fdxN</i> gene, as well as analogous arrangements in other strains, occupy the genetic elements that become excised during the differentiation-related programmed site-specific recombination. This fact indicates the propensity of these elements for the integration of CRISPR-<i>cas</i> systems and points to a previously not recognized connection. The gene <i>all3613</i> resembling a possible Class 2 effector protein is linked to a short repeat-spacer array and a single tRNA gene, similar to its homologs in other cyanobacteria. The diversity and presence of numerous CRISPR-Cas systems in DNA elements that are programmed for homologous recombination make filamentous cyanobacteria a prolific resource for their study. <b>Abbreviations</b>: Cas: CRISPR associated sequences; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; C2c: Class 2 candidate; SDR: small dispersed repeat; TSS: transcriptional start site; UTR: untranslated region.
DOI: 10.6084/m9.figshare.6807134
title: NEON Teaching Data: Modularizing Scripts Data - SJER Hyperspectral Data

description: These three hdf5 files contain hyperspectral information from the NEON Airborne Observation Platform. They are used as part of an exercise on code reproducibility and modularity. They were selected to be of a manageable file size for teaching purposes (~60 MB each vs ~600 MB for a 1000m x 1000m tile).<br><br>This teaching data subset is used for several tutorials on the NEON website (neonscience.org). The dataset is for educational purposes, data for research purposes can be obtained from the NEON Data Portal (data.neonscience.org).
DOI: 10.6084/m9.figshare.6807134.v1
title: NEON Teaching Data: Modularizing Scripts Data - SJER Hyperspectral Data

description: These three hdf5 files contain hyperspectral information from the NEON Airborne Observation Platform. They are used as part of an exercise on code reproducibility and modularity. They were selected to be of a manageable file size for teaching purposes (~60 MB each vs ~600 MB for a 1000m x 1000m tile).<br><br>This teaching data subset is used for several tutorials on the NEON website (neonscience.org). The dataset is for educational purposes, data for research purposes can be obtained from the NEON Data Portal (data.neonscience.org).
DOI: 10.26180/5b46578964c4e
title: Near-wall statistics of the CICLoPE turbulent pipe flow at shear Reynolds numbers up to 40 000.

description: The data presented here are the first and second order statistics of near-wall two-component–two-dimensional (2C–2D) particle image velocimetry (PIV) measurements of a turbulent pipe flow at shear Reynolds numbers up to acquired in the CICLoPE facility of the University of Bologna. The 111.5 m long pipe of 900 mm diameter offers a well-established turbulent flow with viscous length scales ranging from at down to at . These length scales can be resolved with a high-speed PIV camera at image magnification near unity. Statistically converged velocity profiles were determined using multiple sequences of up to 70 000 PIV recordings acquired at sampling rates of 100 Hz up to 10 kHz. Analysis of the velocity statistics shows a well-resolved inner peak of the streamwise velocity fluctuations that grows with increasing Reynolds number and an outer peak that develops and moves away from the inner peak with increasing Reynolds number.<br><br><b>DATAFILES:</b>ASCII tecplot files (include additional experimental information as comments)profile_u05mps.dat: Re_tau = 5,383<b><br></b>profile_u10mps.dat: Re_tau = 11,708<br>profile_u20mps.dat: Re_tau = 19,918<br>profile_u30mps.dat: Re_tau = 27,983<br>profile_u40mps.dat: Re_tau = 39,944<br><br><br><b>PUBLICATION:</b>The experiment and turbulent velocity statistics has been reported in the archival literature: Christian E. Willert, Julio Soria, Michel Stanislas, Joachim Klinner, Omid Amili, Michael Eisfelder, Christophe Cuvier, Gabriele Bellani, Tommaso Fiorini and Alessandro Talamelli (2017). Near-wall statistics of a turbulent pipe flow at shear Reynolds numbers up to 40 000. Journal of Fluid Mechanics, 826, R5. doi:10.1017/jfm.2017.498. <br><br><b>Note:</b> when referring to this data this journal publication must be referred to as well.<br>
DOI: 10.6084/m9.figshare.6806924
title: DistanceMatrix

description: Distance Matrix of Japanese and Chinese population in Hapmap database
DOI: 10.6084/m9.figshare.6806924.v1
title: DistanceMatrix

description: Distance Matrix of Japanese and Chinese population in Hapmap database
DOI: 10.6084/m9.figshare.6804614
title: Deregulation of MADS-box transcription factor genes in a mutant defective in the <i>WUSCHEL-LIKE HOMEOBOX</i> gene <i>EVERGREEN</i> of <i>Petunia hybrida</i>

description: Angiosperm inflorescences develop in two fundamentally different ways. In monopodial plants, for example in <i>Arabidopsis thaliana</i>, the flowers are initiated as lateral appendages of a central indeterminate inflorescence meristem. In sympodial plants, flowers arise by terminal differentiation of the inflorescence meristem, while further inflorescence development proceeds from new sympodial meristems that are generated at the flank of the terminal flower. We have used the sympodial model species <i>Petunia hybrida</i> to investigate inflorescence development. Here, we describe a mutant, <i>bonsai</i> (<i>bns</i>), which is defective in flower formation, inflorescence branching, and control of meristem size. Detailed microscopic analysis revealed that <i>bns</i> meristems retain vegetative charateristics including spiral phyllotaxis. Consistent with a block in flower formation, <i>bns</i> mutants exhibit a deregulated expression of various MADS-box genes. Molecular analysis revealed that the <i>bns</i> mutant carries a transposon insertion in the previously described <i>EVERGREEN</i> (<i>EVG</i>) gene, which belongs to the <i>WUSCHEL-LIKE HOMEOBOX</i> (<i>WOX</i>) transcription factor gene family. <i>EVG</i> falls in the <i>WOX9</i> subfamily, which has diverse developmental functions in angiosperms. The comparison of <i>WOX9</i> orthologues in five model species for flowering shows that these genes play functionally divergent roles in monopodial and sympodial plants, indicating that the <i>WOX9</i> regulatory node may have played an important role in the evolution of shoot architecture.
DOI: 10.6084/m9.figshare.6804614.v1
title: Deregulation of MADS-box transcription factor genes in a mutant defective in the <i>WUSCHEL-LIKE HOMEOBOX</i> gene <i>EVERGREEN</i> of <i>Petunia hybrida</i>

description: Angiosperm inflorescences develop in two fundamentally different ways. In monopodial plants, for example in <i>Arabidopsis thaliana</i>, the flowers are initiated as lateral appendages of a central indeterminate inflorescence meristem. In sympodial plants, flowers arise by terminal differentiation of the inflorescence meristem, while further inflorescence development proceeds from new sympodial meristems that are generated at the flank of the terminal flower. We have used the sympodial model species <i>Petunia hybrida</i> to investigate inflorescence development. Here, we describe a mutant, <i>bonsai</i> (<i>bns</i>), which is defective in flower formation, inflorescence branching, and control of meristem size. Detailed microscopic analysis revealed that <i>bns</i> meristems retain vegetative charateristics including spiral phyllotaxis. Consistent with a block in flower formation, <i>bns</i> mutants exhibit a deregulated expression of various MADS-box genes. Molecular analysis revealed that the <i>bns</i> mutant carries a transposon insertion in the previously described <i>EVERGREEN</i> (<i>EVG</i>) gene, which belongs to the <i>WUSCHEL-LIKE HOMEOBOX</i> (<i>WOX</i>) transcription factor gene family. <i>EVG</i> falls in the <i>WOX9</i> subfamily, which has diverse developmental functions in angiosperms. The comparison of <i>WOX9</i> orthologues in five model species for flowering shows that these genes play functionally divergent roles in monopodial and sympodial plants, indicating that the <i>WOX9</i> regulatory node may have played an important role in the evolution of shoot architecture.
DOI: 10.6084/m9.figshare.6804566
title: Worksheet for Galactic Distribution of Chirality Sources of Organic Molecules

description: This is the supplemental worksheet associated with the article "Galactic Distribution of Chirality Sources of Organic Molecules" https://doi.org/10.1016/j.actaastro.2018.07.008
DOI: 10.6084/m9.figshare.6804566.v1
title: Worksheet for Galactic Distribution of Chirality Sources of Organic Molecules

description: This is the supplemental worksheet associated with the article "Galactic Distribution of Chirality Sources of Organic Molecules" https://doi.org/10.1016/j.actaastro.2018.07.008
DOI: 10.6084/m9.figshare.6804518
title: Lateral root growth in Arabidopsis is controlled by short and long distance signaling through the LRR RLKs XIP1/CEPR1 and CEPR2

description: Plants rely on lateral roots to explore their soil environment and to maximize their uptake of essential minerals and water. Here we present evidence that the receptor kinases XIP1/CEPR1 and CEPR2 regulate both the initiation of lateral root primordia and emergence of lateral roots locally in the root, while also controlling lateral root extension in response to shoot-derived sucrose in Arabidopsis plants. In addition, mutation of both of these receptors prevents seedlings from responding to sucrose in the media, resulting in longer lateral roots. These results, combined with previous data, establish XIP1/CEPR1 and CEPR2-dependent roles in short- and long-distance pathways regulating different stages of lateral root growth.
DOI: 10.6084/m9.figshare.6804518.v1
title: Lateral root growth in Arabidopsis is controlled by short and long distance signaling through the LRR RLKs XIP1/CEPR1 and CEPR2

description: Plants rely on lateral roots to explore their soil environment and to maximize their uptake of essential minerals and water. Here we present evidence that the receptor kinases XIP1/CEPR1 and CEPR2 regulate both the initiation of lateral root primordia and emergence of lateral roots locally in the root, while also controlling lateral root extension in response to shoot-derived sucrose in Arabidopsis plants. In addition, mutation of both of these receptors prevents seedlings from responding to sucrose in the media, resulting in longer lateral roots. These results, combined with previous data, establish XIP1/CEPR1 and CEPR2-dependent roles in short- and long-distance pathways regulating different stages of lateral root growth.
DOI: 10.6084/m9.figshare.6804500
title: Multiple macroevolutionary routes to becoming a biodiversity hotspot - Scripts and files

description: Scripts and files for "Multiple macroevolutionary routes to becoming a biodiversity hotspot" by J. Igea and A.J. TanentzapFor more updated version please go to https://github.com/javierigea/hotspots_mambird_paper
DOI: 10.6084/m9.figshare.6804491
title: Efficient Covariance Approximations for Large Sparse Precision Matrices

description: The use of sparse precision (inverse covariance) matrices has become popular because they allow for efficient algorithms for joint inference in high-dimensional models. Many applications require the computation of certain elements of the covariance matrix, such as the marginal variances, which may be nontrivial to obtain when the dimension is large. This article introduces a fast Rao–Blackwellized Monte Carlo sampling-based method for efficiently approximating selected elements of the covariance matrix. The variance and confidence bounds of the approximations can be precisely estimated without additional computational costs. Furthermore, a method that iterates over subdomains is introduced, and is shown to additionally reduce the approximation errors to practically negligible levels in an application on functional magnetic resonance imaging data. Both methods have low memory requirements, which is typically the bottleneck for competing direct methods.
DOI: 10.6084/m9.figshare.6804491.v2
title: Efficient Covariance Approximations for Large Sparse Precision Matrices

description: The use of sparse precision (inverse covariance) matrices has become popular because they allow for efficient algorithms for joint inference in high-dimensional models. Many applications require the computation of certain elements of the covariance matrix, such as the marginal variances, which may be nontrivial to obtain when the dimension is large. This article introduces a fast Rao–Blackwellized Monte Carlo sampling-based method for efficiently approximating selected elements of the covariance matrix. The variance and confidence bounds of the approximations can be precisely estimated without additional computational costs. Furthermore, a method that iterates over subdomains is introduced, and is shown to additionally reduce the approximation errors to practically negligible levels in an application on functional magnetic resonance imaging data. Both methods have low memory requirements, which is typically the bottleneck for competing direct methods.
DOI: 10.6084/m9.figshare.6804491.v1
title: Efficient Covariance Approximations for Large Sparse Precision Matrices

description: The use of sparse precision (inverse covariance) matrices has become popular because they allow for efficient algorithms for joint inference in high-dimensional models. Many applications require the computation of certain elements of the covariance matrix, such as the marginal variances, which may be non-trivial to obtain when the dimension is large. This paper introduces a fast Rao-Blackwellized Monte Carlo sampling-based method for efficiently approximating selected elements of the covariance matrix. The variance and confidence bounds of the approximations can be precisely estimated without additional computational costs. Furthermore, a method that iterates over subdomains is introduced, and is shown to additionally reduce the approximation errors to practically negligible levels in an application on functional magnetic resonance imaging data. Both methods have low memory requirements, which is typically the bottleneck for competing direct methods.
DOI: 10.6084/m9.figshare.6804386
title: Smart Grids Data Analysis: A Systematic Mapping Study

description: Supporting material for the article <i>"Smart Grids Data Analysis: A Systematic Mapping Study"</i> accepted for publication in IEEE Transaction of Industrial Informatics journal. In this material, you can find the list with references of the 359 papers included.<br><br>The review includes 359 papers, initially 267 papers were reviewed, and a 2nd round increased the number. Additional diagrams to those included in the paper refer to this first round. After the paper was reviewed, new papers from 2018-2019 were added (92). The final outcome of the review is a total of 359 articles (2007-2019).<br> Included files:------------------<br>+ <b>SMS-PapersList.pdf</b>: list of included papes in the SMS with the index used in the article;+ <b>SMS-PapersList-Small.pdf</b>: same list, but with smaller font (less pages) + <b>SMS-Mined-Scopus-IEEE-ACM-WoS-SpringerLink-ScienceDirect.zip</b>: bib files from the 2129 articles mined from the digital repositories at the beginning of the SMS process;+ <b>SMS-Filtered-267-bib.zip</b>: bib files from the 267 SMS articles with metadata about the SMS categories (using JabRef version 2.10b2);<br>+ <b>SMS-Abstracts-267papers.zip</b>: abstracts from the 267 SMS articles;+ <b>SMS-2018-2019-bib-Addendum.zip</b>: contains an addendum of articles (92) in bib format that were added after the paper was reviewed to include articles from 2018-2019.+ <b>SMS-Top-Terms-Bigrams-Trigrams-csv.zip</b>: csv files with the top terms, bigrams, trigrams from all the categories;+ <b>SMS-source.zip</b>: R source code for bubble-plots and for text-mining (environment used: RStudio 1.1.383, R version 3.4.4 (2018-03-15) platform x86_64-pc-linux-gnu, Ubuntu 14.04 kernel 3.13.0-153);<br>+ <b>SMS-HiRes-Images.zip</b>: high resolution figures;+ <b>SMS-top-trigrams.png, </b><b>SMS-top-bigrams.png, SMS-top-terms.png</b>: graphics for all the top terms in the abstracts;
DOI: 10.22023/mdx.6804359
title: Artist's Impression: Mangled Metal

description: Scatter piece sculpture installed at Peltz Gallery, Birkbeck, University of London, July 2015.<br>This art work, which was produced during a residency funded by Bow Arts Trust and the Peltz Gallery at Birkbeck, arose out of conversations with Dr Gabriel Kourias about his research on gender, masculinities and histories of conflict. The forms were constructed from paint and cardboard, researching documentary photographs of wreckage from car bombs found in the photographic archive of the Imperial War Museum, London.<br><br>(Photograph credit: Dominic Milfsud)<br>
DOI: 10.6084/m9.figshare.6804326
title: Brain lower grade Glioma

description: microRNA expression of Brain lower grade Glioma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804332
title: Skin cutaneous melanoma

description: microRNA expression of Skin cutaneous melanoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804332.v1
title: Skin cutaneous melanoma

description: microRNA expression of Skin cutaneous melanoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804326.v1
title: Brain lower grade Glioma

description: microRNA expression of Brain lower grade Glioma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804242
title: Breast invasive carcinoma

description: microRNA expression of Breast invasive carcinoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804242.v1
title: Breast invasive carcinoma

description: microRNA expression of Breast invasive carcinoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804233
title: Liver hepatocellular carcinoma

description: microRNA expression of Liver hepatocellular carcinoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804233.v1
title: Liver hepatocellular carcinoma

description: microRNA expression of Liver hepatocellular carcinoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804206
title: Thyroid carcinoma

description: microRNA expression of Thyroid carcinoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804212
title: Prostate adenocarcinoma

description: microRNA expression of Prostate adenocarcinoma samples. Data from TGCA (https://cancergenome.nih.gov/)
DOI: 10.6084/m9.figshare.6804206.v1
title: Thyroid carcinoma

description: microRNA expression of Thyroid carcinoma samples. Data from TGCA (https://cancergenome.nih.gov/)