cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5663134
title: A hegemony of 'blame and fault' in the intergenerational transmission of Pacific languages

description: This paper was presented at ITML3 http://latllab.canterbury.ac.nz/intergenerational-transmission-pacific-languages-aotearoa-nz/<br><br>The intergenerational transmission of all Pacific languages in Aotearoa NZ is now becoming seriously at risk due to the continuing lack of recognition, status and prestige in the Civic Domain which is largely controlled by (successive) governments and their agencies. In this paper we update our current state 2010 Alternative (6) article on the overview of Pacific languages in Aotearoa NZ and our 2013 Census analysis. We argue now that in spite of many important initiatives by Pacific communities since 2010 that because of this lack of status in the Civic Domain, Pacific youth and many communities continue to see our languages as the languages of older generations, suitable mainly for home and church and largely unsuited for work, education and the future.<br> <br> <br> <br> <br>Judy Taligalu McFall-McCaffery|Pasifika Librarian|Researcher Maori & Pasifika Information Services|GeneralLibrary|The University of Auckland|Private Bag 92019|Auckland 1142|New Zealand|Ph:(649) 373 7599 X 83165 Mob +64 272083766 email: j.mcfall@auckland.ac.nz|http://www.library.auckland.ac.nz/subjects/pasifika/pasifikasubj.htm<br> <br> <br>John McCaffery. Hon Academic -Researcher –Consultant –Doctoral Candidate <br>Bilingual/ Biliteracy Immersion Education Te Puna Wananga – School of Måori and Indigenous Studies, Faculty of Education, Epsom Campus. University of Auckland , Private Bag 92601, Symonds Street, Auckland 1, Aotearoa/New Zealand email: j.mccaffery@auckland.ac.nz jmcc084@aucklanduni.ac.nz Work: +64 27 20 83 766 Mob: 027 20 83 766 <br> https://twitter.com/JohnMcCafferyNZ <br><br>
DOI: 10.6084/m9.figshare.5663134.v1
title: A hegemony of 'blame and fault' in the intergenerational transmission of Pacific languages

description: This paper was presented at ITML3 http://latllab.canterbury.ac.nz/intergenerational-transmission-pacific-languages-aotearoa-nz/<br><br>The intergenerational transmission of all Pacific languages in Aotearoa NZ is now becoming seriously at risk due to the continuing lack of recognition, status and prestige in the Civic Domain which is largely controlled by (successive) governments and their agencies. In this paper we update our current state 2010 Alternative (6) article on the overview of Pacific languages in Aotearoa NZ and our 2013 Census analysis. We argue now that in spite of many important initiatives by Pacific communities since 2010 that because of this lack of status in the Civic Domain, Pacific youth and many communities continue to see our languages as the languages of older generations, suitable mainly for home and church and largely unsuited for work, education and the future.<br> <br> <br> <br> <br>Judy Taligalu McFall-McCaffery|Pasifika Librarian|Researcher Maori & Pasifika Information Services|GeneralLibrary|The University of Auckland|Private Bag 92019|Auckland 1142|New Zealand|Ph:(649) 373 7599 X 83165 Mob +64 272083766 email: j.mcfall@auckland.ac.nz|http://www.library.auckland.ac.nz/subjects/pasifika/pasifikasubj.htm<br> <br> <br>John McCaffery. Hon Academic -Researcher –Consultant –Doctoral Candidate <br>Bilingual/ Biliteracy Immersion Education Te Puna Wananga – School of Måori and Indigenous Studies, Faculty of Education, Epsom Campus. University of Auckland , Private Bag 92601, Symonds Street, Auckland 1, Aotearoa/New Zealand email: j.mccaffery@auckland.ac.nz jmcc084@aucklanduni.ac.nz Work: +64 27 20 83 766 Mob: 027 20 83 766 <br> https://twitter.com/JohnMcCafferyNZ <br><br>
DOI: 10.6084/m9.figshare.5662741
title: Arctic char transcriptome annotations

description: Two annotation tables that for a liver transcriptome of Arctic char (<i>Salvelinus alpinus</i>) (Prokkola et al). The de novo assembly available at DDBJ/EMBL/GenBank under the accession GEKT00000000. Open reading frame (ORF) peptide sequences were obtained for transcripts in the final assembly using TransDecoder. The predicted ORFs were annotated with four databases using Basic Local Alignment Search Tool for proteins (BLASTp v.2.2.31): predicted zebrafish (downloaded Oct 24 2015 from Ensembl) and salmon (NCBI <i>Salmo salar</i> Annotation Release 100) proteins using a reciprocal best hits approach and an e-value cutoff 1x10<sup>-5</sup>. Additionally, the ORFs were annotated with NCBI non-redundant protein database (downloaded Nov 25<sup>th</sup> 2015) with e-value cutoff 1x10<sup>-5</sup> and when the query sequence matched the target sequence at &gt;50 % protein length, and with human peptides. The first file (Annotations_Salp...") contains results that were prioritized with the order zebrafish &gt; salmon &gt; NCBI nr. When available, gene descriptions were retrieved from Ensembl using biomaRt in R. Gene symbols were retrieved for zebrafish Ensembl IDs, salmon Refseq IDs and NCBI gene names using Biological DataBase Network (https://biodbnet-abcc.ncifcrf.gov). Annotations were retrieved for 9,491, 4,037 and 4,117 genes with zebrafish peptides, Atlantic salmon predicted peptides and the NCBI nr-database, respectively. In total, 20,394 out of 44,784 ORFs in the assembly (45.5%) were annotated with 18,013 unique protein IDs. The second table contains all gene symbols found for the above mentioned fish or for human peptide sequences using BLASTp v.2.4.0 with an E-value threshold 10<sup>-5</sup>. After identifying human orthologs, we supplemented the annotation by the previously obtained gene symbols for genes that were missing an annotation. In total 18,232 genes were annotated using this approach with 9,577 unique gene symbols.<br>
DOI: 10.6084/m9.figshare.5662741.v1
title: Arctic char transcriptome annotations

description: Two annotation tables that for a liver transcriptome of Arctic char (<i>Salvelinus alpinus</i>) (Prokkola et al). The de novo assembly available at DDBJ/EMBL/GenBank under the accession GEKT00000000. Open reading frame (ORF) peptide sequences were obtained for transcripts in the final assembly using TransDecoder. The predicted ORFs were annotated with four databases using Basic Local Alignment Search Tool for proteins (BLASTp v.2.2.31): predicted zebrafish (downloaded Oct 24 2015 from Ensembl) and salmon (NCBI <i>Salmo salar</i> Annotation Release 100) proteins using a reciprocal best hits approach and an e-value cutoff 1x10<sup>-5</sup>. Additionally, the ORFs were annotated with NCBI non-redundant protein database (downloaded Nov 25<sup>th</sup> 2015) with e-value cutoff 1x10<sup>-5</sup> and when the query sequence matched the target sequence at &gt;50 % protein length, and with human peptides. The first file (Annotations_Salp...") contains results that were prioritized with the order zebrafish &gt; salmon &gt; NCBI nr. When available, gene descriptions were retrieved from Ensembl using biomaRt in R. Gene symbols were retrieved for zebrafish Ensembl IDs, salmon Refseq IDs and NCBI gene names using Biological DataBase Network (https://biodbnet-abcc.ncifcrf.gov). Annotations were retrieved for 9,491, 4,037 and 4,117 genes with zebrafish peptides, Atlantic salmon predicted peptides and the NCBI nr-database, respectively. In total, 20,394 out of 44,784 ORFs in the assembly (45.5%) were annotated with 18,013 unique protein IDs. The second table contains all gene symbols found for the above mentioned fish or for human peptide sequences using BLASTp v.2.4.0 with an E-value threshold 10<sup>-5</sup>. After identifying human orthologs, we supplemented the annotation by the previously obtained gene symbols for genes that were missing an annotation. In total 18,232 genes were annotated using this approach with 9,577 unique gene symbols.<br>
DOI: 10.6084/m9.figshare.5662498
title: Testing clumped isotopes as a reservoir characterization tool: a comparison with fluid inclusions in a dolomitized sedimentary carbonate reservoir buried to 2–4 km

description: All standard and sample data.
DOI: 10.6084/m9.figshare.5662498.v1
title: Testing clumped isotopes as a reservoir characterization tool: a comparison with fluid inclusions in a dolomitized sedimentary carbonate reservoir buried to 2–4 km

description: All standard and sample data.
DOI: 10.6084/m9.figshare.5662489
title: Arctic char log read counts

description: Read counts from RNA-sequencing experiment in Arctic char (Prokkola et al.). Rows correspond to genes and columns correspond to samples. Reads can be downloaded from NCBI SRA (accession SRP068854). The used reference is available at DDBJ/EMBL/GenBank under the accession GEKT00000000. The trimmed PE reads from all samples were aligned against the assembly using Bowtie2, ignoring discordant and mixed alignments and allowing a maximum of 40 multiple alignments per read. Read counts per cluster were obtained using Corset (Davidson and Oshlack 2014). Clusters that were expressed with &gt;1 counts per million reads (cpm) in at least 3 samples across all 18 samples were included in the analysis. Data were normalized for library sizes in Studio using edgeR package TMM-normalization (Robinson and Oshlack 2010) and normalized log counts of reads per million mapped reads in each sample exported.
DOI: 10.6084/m9.figshare.5662489.v1
title: Arctic char log read counts

description: Read counts from RNA-sequencing experiment in Arctic char (Prokkola et al.). Rows correspond to genes and columns correspond to samples. Reads can be downloaded from NCBI SRA (accession SRP068854). The used reference is available at DDBJ/EMBL/GenBank under the accession GEKT00000000. The trimmed PE reads from all samples were aligned against the assembly using Bowtie2, ignoring discordant and mixed alignments and allowing a maximum of 40 multiple alignments per read. Read counts per cluster were obtained using Corset (Davidson and Oshlack 2014). Clusters that were expressed with &gt;1 counts per million reads (cpm) in at least 3 samples across all 18 samples were included in the analysis. Data were normalized for library sizes in Studio using edgeR package TMM-normalization (Robinson and Oshlack 2010) and normalized log counts of reads per million mapped reads in each sample exported.
DOI: 10.6084/m9.figshare.5662396
title: Data for Marginal Effects Graph

description: This data is used to generate the marginal effects graph (figure 3 in the paper) using the code that is also provided in this folder.
DOI: 10.6084/m9.figshare.5662396.v1
title: Data for Marginal Effects Graph

description: This data is used to generate the marginal effects graph (figure 3 in the paper) using the code that is also provided in this folder.
DOI: 10.6084/m9.figshare.5662393
title: ILD data

description: This is the data of subjects with interstitial lung diseases from a tertiary care center ion northern India<br>
DOI: 10.6084/m9.figshare.5662384
title: RNA polymerases IV and V influence the 3′ boundaries of Polymerase II transcription units in <i>Arabidopsis</i>

description: Nuclear multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved in plants as specialized forms of Pol II. Their functions are best understood in the context of RNA-directed DNA methylation (RdDM), a process in which Pol IV-dependent 24 nt siRNAs direct the <i>de novo</i> cytosine methylation of regions transcribed by Pol V. Pol V has additional functions, independent of Pol IV and 24 nt siRNA biogenesis, in maintaining the repression of transposons and genomic repeats whose silencing depends on maintenance cytosine methylation. Here we report that Pol IV and Pol V play unexpected roles in defining the 3′ boundaries of Pol II transcription units. Nuclear run-on assays reveal that in the absence of Pol IV or Pol V, Pol II occupancy downstream of poly A sites increases for approximately 12% of protein-coding genes. This effect is most pronounced for convergently transcribed gene pairs. Although Pols IV and V are detected near transcript ends of the affected Pol II – transcribed genes, their role in limiting Pol II read-through is independent of siRNA biogenesis or cytosine methylation for the majority of these genes. Interestingly, we observed that splicing was less efficient in <i>pol IV</i> or <i>pol V</i> mutant plants, compared to wild-type plants, suggesting that Pol IV or Pol V might affect pre-mRNA processing. We speculate that Pols IV and V (and/or their associated factors) play roles in Pol II transcription termination and pre-mRNA splicing by influencing polymerase elongation rates and/or release at collision sites for convergent genes.
DOI: 10.6084/m9.figshare.5662384.v1
title: <b>RNA polymerases IV and V influence the 3’ boundaries of Polymerase II transcription units in <i>Arabidopsis</i></b>

description: Nuclear multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved in plants as specialized forms of Pol II. Their functions are best understood in the context of RNA-directed DNA methylation (RdDM), a process in which Pol IV-dependent 24 nt siRNAs direct the <i>de novo</i> cytosine methylation of regions transcribed by Pol V. Pol V has additional functions, independent of Pol IV and 24 nt siRNA biogenesis, in maintaining the repression of transposons and genomic repeats whose silencing depends on maintenance cytosine methylation. Here we report that Pol IV and Pol V play unexpected roles in defining the 3’ boundaries of Pol II transcription units. Nuclear run-on assays reveal that in the absence of Pol IV or Pol V, Pol II occupancy downstream of poly A sites increases for approximately 12% of protein-coding genes. This effect is most pronounced for convergently transcribed gene pairs. Although Pols IV and V are detected near transcript ends of the affected Pol II – transcribed genes, their role in limiting Pol II read-through is independent of siRNA biogenesis or cytosine methylation for the majority of these genes. Interestingly, we observed that splicing was less efficient in <i>pol IV</i> or <i>pol V</i> mutant plants, compared to wild-type plants, suggesting that Pol IV or Pol V might affect pre-mRNA processing. We speculate that Pols IV and V (and/or their associated factors) play roles in Pol II transcription termination and pre-mRNA splicing by influencing polymerase elongation rates and/or release at collision sites for convergent genes.
DOI: 10.6084/m9.figshare.5662375
title: Summary of Results: Marginal Effects

description: This file summarizes the results of the marginal effects analysis for policy variables education, wealth, improved sanitation, improved water and upstream tree cover.
DOI: 10.6084/m9.figshare.5662375.v1
title: Summary of Results: Marginal Effects

description: This file summarizes the results of the marginal effects analysis for policy variables education, wealth, improved sanitation, improved water and upstream tree cover.
DOI: 10.6084/m9.figshare.5662339
title: experiment data (Discretized Theta-Rhythm Perception Revealed by Moving Stimuli)

description: experiment data (exp1-3)
DOI: 10.6084/m9.figshare.5662339.v1
title: exp data (Discretized Theta-Rhythm Perception Revealed by Moving Stimuli)

description: experiment data (exp1-3)
DOI: 10.6084/m9.figshare.5662339.v3
title: experiment data (Discretized Theta-Rhythm Perception Revealed by Moving Stimuli)

description: experiment data (exp1-3)
DOI: 10.6084/m9.figshare.5662339.v2
title: exp data (Discretized Theta-Rhythm Perception Revealed by Moving Stimuli)

description: experiment data (exp1-3)
DOI: 10.6084/m9.figshare.5662312
title: Jerash Interpretation

description: Vectorised interpretations of possible archaeological features identified in airborne remote sensing (airborne laser scanning and aerial photographs dating back to 1917).<br>Used in the following article:<br>Stott, D., Kristiansen, S.M., Lichtenberger, A. and Raja, R., 2018. Mapping an ancient city with a century of remotely sensed data. <i>Proceedings of the National Academy of Sciences</i>, <i>115</i>(24), pp.E5450-E5458.<br><br>
DOI: 10.6084/m9.figshare.5662312.v1
title: Jerash Interpretation

description: Vectorised interpretations of possible archaeological features identified in airborne remote sensing (airborne laser scanning and aerial photographs dating back to 1917).<br><br><br>
DOI: 10.6084/m9.figshare.5662312.v2
title: Jerash Interpretation

description: Vectorised interpretations of possible archaeological features identified in airborne remote sensing (airborne laser scanning and aerial photographs dating back to 1917).<br>Used in the following article:<br>Stott, D., Kristiansen, S.M., Lichtenberger, A. and Raja, R., 2018. Mapping an ancient city with a century of remotely sensed data. <i>Proceedings of the National Academy of Sciences</i>, <i>115</i>(24), pp.E5450-E5458.<br><br>
DOI: 10.6084/m9.figshare.5662312.v3
title: Jerash Interpretation

description: Vectorised interpretations of possible archaeological features identified in airborne remote sensing (airborne laser scanning and aerial photographs dating back to 1917).<br>Used in the following article:<br>Stott, D., Kristiansen, S.M., Lichtenberger, A. and Raja, R., 2018. Mapping an ancient city with a century of remotely sensed data. <i>Proceedings of the National Academy of Sciences</i>, <i>115</i>(24), pp.E5450-E5458.<br><br>
DOI: 10.6084/m9.figshare.5662306
title: A walk in the maze: Variation in Late Jurassic tridactyl dinosaur tracks from the Swiss Jura Mountains (NW Switzerland). 3D photogrammetric models

description: All the collected and/or casted specimens, are stored and accessible at the PALA16 collections (Office de la Culture, 2900, Porrentruy, Switzerland) and will be transferred to the JURASSICA Muséum (Route de Fontenais 21, 2900, Porrentruy, Switzerland) at the end of 2018.Files are labelled accordingly the individual track IDs.<br><br> All photogrammetric models were generated with a Canon EOS 70D thought Agisoft Photoscan Pro (v. 1.3.2); number of photos used, accuracy and resolution of each models are in the associated pdf. "laser" in the file name indicates tracks that were laser-scanned in 2011 with a FARO Platinum Scanarm 3.0 m. Processing information in the associated pdf.<br> <b><i>Citation for this article</i></b>: Castanera D., Belvedere M., Marty D., Paratte G., Lovis C., Cattin M., and Meyer C.A. 2018. A walk in the maze: Variation in Late Jurassic tridactyl dinosaur tracks - A case study from the Late Jurassic of the Swiss Jura Mountains (NW Switzerland). PeerJ
DOI: 10.6084/m9.figshare.5662306.v1
title: A walk in the maze: Variation in Late Jurassic tridactyl dinosaur tracks - A case study from the Late Jurassic of the Swiss Jura Mountains (NW Switzerland). 3D photogrammetric models

description: All the collected and/or casted specimens, are stored and accessible at the PALA16 collections (Office de la Culture, 2900, Porrentruy, Switzerland) and will be transferred to the JURASSICA Muséum (Route de Fontenais 21, 2900, Porrentruy, Switzerland) at the end of 2018.Files are labelled accordingly the individual track IDs.<br><br> All photogrammetric models were generated with a Canon EOS 70D thought Agisoft Photoscan Pro (v. 1.3.2); number of photos used, accuracy and resolution of each models are in the associated pdf. "laser" in the file name indicates tracks that were laser-scanned in 2011 with a FARO Platinum Scanarm 3.0 m. Processing information in the associated pdf.<br> <b><i>Citation for this article</i></b>: Castanera D., Belvedere M., Marty D., Paratte G., Lovis C., Cattin M., and Meyer C.A. 2018. A walk in the maze: Variation in Late Jurassic tridactyl dinosaur tracks - A case study from the Late Jurassic of the Swiss Jura Mountains (NW Switzerland). PeerJ
DOI: 10.6084/m9.figshare.5662282
title: Dataset1 and putative SNPs under selection

description: Dataset 1 contains the called genotypes for 60 plains zebras, 3 Grevy's zebras, 3 mountain zebras and one Quagga zebra. A total of 98,512 SNPs were called. The data is based on the RADseq technology. We used a missingness filter of 0.2 and excluded monomorphic sites.<br>We also include a list of SNPs putatively under selection<br><br>
DOI: 10.6084/m9.figshare.5662267
title: Dataset for: Meta-analysis of quantitative individual patient data: two stage or not two stage?

description: Quantitative evidence synthesis through meta-analysis is central to evidence-based medicine. For well-documented reasons, the meta-analysis of individual patient data (IPD) is held in higher regard than aggregate data. With access to IPD, the analysis is not restricted to a ‘two-stage’ approach (combining estimates and standard errors) but can estimate parameters of interest by fitting a single model to all of the data; a so-called ‘one-stage’ analysis. There has been debate about the merits of one- and two-stage analysis. Arguments for one-stage analysis have typically noted that a wider range of models can be fitted and overall estimates may be more precise. The two-stage side has emphasised that the models that can be fitted in two-stages are sufficient to answer the relevant questions, with less scope less scope for mistakes because there are fewer modelling choices to be made in the two-stage approach. Considering Gaussian data, we consider the statistical arguments for flexibility and precision in the small-sample settings. Regarding flexibility, several of the models that can be fitted only in one stage may not be of serious interest to most meta-analysis practitioners. Regarding precision, we consider fixed- and random-effects meta-analysis, and see that, for a model making certain assumptions, the number of stages used to fit this model is irrelevant; the precision will be approximately equal. Meta-analysts should choose modelling assumptions carefully. Sometimes relevant models can only be fitted in one stage. Otherwise, meta-analysts are free to use whichever procedure is most convenient to fit the identified model.
DOI: 10.6084/m9.figshare.5662267.v1
title: Dataset for: Meta-analysis of quantitative individual patient data: two stage or not two stage?

description: Quantitative evidence synthesis through meta-analysis is central to evidence-based medicine. For well-documented reasons, the meta-analysis of individual patient data (IPD) is held in higher regard than aggregate data. With access to IPD, the analysis is not restricted to a ‘two-stage’ approach (combining estimates and standard errors) but can estimate parameters of interest by fitting a single model to all of the data; a so-called ‘one-stage’ analysis. There has been debate about the merits of one- and two-stage analysis. Arguments for one-stage analysis have typically noted that a wider range of models can be fitted and overall estimates may be more precise. The two-stage side has emphasised that the models that can be fitted in two-stages are sufficient to answer the relevant questions, with less scope less scope for mistakes because there are fewer modelling choices to be made in the two-stage approach. Considering Gaussian data, we consider the statistical arguments for flexibility and precision in the small-sample settings. Regarding flexibility, several of the models that can be fitted only in one stage may not be of serious interest to most meta-analysis practitioners. Regarding precision, we consider fixed- and random-effects meta-analysis, and see that, for a model making certain assumptions, the number of stages used to fit this model is irrelevant; the precision will be approximately equal. Meta-analysts should choose modelling assumptions carefully. Sometimes relevant models can only be fitted in one stage. Otherwise, meta-analysts are free to use whichever procedure is most convenient to fit the identified model.