cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5691388
title: Additional file 10: Category 2. of The asymmetric cell division machinery in the spiral-cleaving egg and embryo of the marine annelid Platynereis dumerilii

description: Spindle Orientation genes. Individual developmental expression profiles for each ACD gene including standard deviation error bars for all time points are shown. (XLSX 102Â kb)
DOI: 10.6084/m9.figshare.5691388.v1
title: Additional file 10: Category 2. of The asymmetric cell division machinery in the spiral-cleaving egg and embryo of the marine annelid Platynereis dumerilii

description: Spindle Orientation genes. Individual developmental expression profiles for each ACD gene including standard deviation error bars for all time points are shown. (XLSX 102Â kb)
DOI: 10.6084/m9.figshare.5691259
title: Gomez-Casanovas et al_EAP16-0667

description: <pre>Description: Environmental (air temperature and precipitation) and soil variables (soil temperature and moisture) along with CO<sub>2</sub> and CH<sub>4</sub> fluxes for both grazed and ungrazed pastures.</pre><pre> Environmental variables: Air temperature and precipitation values provided are daily averages. </pre><pre> Soil variables: Soil temperature and moisture values provided are daily averages measured at 10 and 15-cm depth, respectively. </pre><pre> CO<sub>2</sub> and CH<sub>4</sub> fluxes provided are half-hour gap filled values. Fluxes of CO<sub>2</sub> were gap filled using the Eddy covariance gap-filling and flux partitioning online tool (http://www.bgc-jena.mpg.de/~MDIwork/eddyproc/index.php), and the fluxes of CH<sub>4</sub> were gap filled replacing missing values by the mean of specific half-hour of four adjacent days. Details of post-processing and gap filling methods are provided in Material and Methods. </pre>
DOI: 10.6084/m9.figshare.5691259.v1
title: Gomez-Casanovas et al_EAP16-0667

description: <pre>Description: Environmental (air temperature and precipitation) and soil variables (soil temperature and moisture) along with CO<sub>2</sub> and CH<sub>4</sub> fluxes for both grazed and ungrazed pastures.</pre><pre> Environmental variables: Air temperature and precipitation values provided are daily averages. </pre><pre> Soil variables: Soil temperature and moisture values provided are daily averages measured at 10 and 15-cm depth, respectively. </pre><pre> CO<sub>2</sub> and CH<sub>4</sub> fluxes provided are half-hour gap filled values. Fluxes of CO<sub>2</sub> were gap filled using the Eddy covariance gap-filling and flux partitioning online tool (http://www.bgc-jena.mpg.de/~MDIwork/eddyproc/index.php), and the fluxes of CH<sub>4</sub> were gap filled replacing missing values by the mean of specific half-hour of four adjacent days. Details of post-processing and gap filling methods are provided in Material and Methods. </pre>
DOI: 10.17608/k6.auckland.5691193
title: Chapter 5, The Gradient

description: A jupyter notebook to illustrate the mathematical concept of the Gradient of a scalar function, applied to topography data from the Auckland Volcanic Field.
DOI: 10.17608/k6.auckland.5691193.v3
title: Chapter 5, The Gradient

description: A jupyter notebook to illustrate the mathematical concept of the Gradient of a scalar function, applied to topography data from the Auckland Volcanic Field.
DOI: 10.17608/k6.auckland.5691193.v2
title: Chapter 5, The Gradient

description: A jupyter notebook to illustrate the mathematical concept of the Gradient of a scalar function, applied to topography data from the Auckland Volcanic Field.
DOI: 10.6084/m9.figshare.5690878
title: Data sharing in PLOS ONE: An analysis of Data Availability Statements

description: This dataset contains Data Availability Statements from 47,593 papers published in PLOS ONE between March 2014 (when the policy went into effect) and May 2016, analyzed for type of statement.<br>
DOI: 10.6084/m9.figshare.5690851
title: mass_spec_comparison_reports.zip

description: These are the statistical comparison reports of significant antibiotic abundance differences in environmental stream and wastewater samples. Fold change and p values are shown.
DOI: 10.6084/m9.figshare.5690851.v1
title: mass_spec_comparison_reports.zip

description: These are the statistical comparison reports of significant antibiotic abundance differences in environmental stream and wastewater samples. Fold change and p values are shown.
DOI: 10.24376/rd.sgul.5689021
title: Researcher perspectives on the challenges facing RRCTs in surgery - qualitative interview data

description: This fileset contains qualitative interview data from a research study sponsored by the University of Edinburgh investigating researcher perspectives on challenges facing the implementation of Registry-based randomised clinical trials in surgical research. Original transcripts (anonymised) organised into themes and categories using the framework method of thematic analysis are included in the fileset. Analytical framework included. Data organised into charts according to theme and category are also provided. Interviews conducted based on a topic guide (included in fileset) for semi-structured in-depth interviews. Ethical review and approval granted by the School of Health and Social Sciences, University of Edinburgh.
DOI: 10.6084/m9.figshare.5688982
title: Appendix 1-figure 9: Ppyr1.2 Blobtools results

description: Given the recognized importance of filtering genome assemblies to avoid misinterpretation of the data, we sought to systematically remove assembled non-firefly contaminant sequence from Ppyr1.2. Using the blobtools toolset (v.1.0.1), we taxonomically annotated our scaffolds by performing a blastn (v2.6.0+) nucleotide sequence similarity search against the NCBI nt database, and a diamond (v.0.9.10.111) translated nucleotide sequence similarity search against the of Uniprot reference proteomes (July 2017). Using this similarity information, we annotated the scaffolds with blobtools using parameters “-x bestsumorder --rank phylum”.
DOI: 10.6084/m9.figshare.5688952
title: Appendix 3-figure 3: Ilumi1.0 Blobtools results

description: We sought to systematically remove assembled non-elaterid contaminant sequence from Ilumi1.0. Using the blobtools toolset (v.1.0.1), we taxonomically annotated our scaffolds by performing a blastn (v2.6.0+) nucleotide sequence similarity search against the NCBI nt database, and a diamond (v.0.9.10.111) translated nucleotide sequence similarity search against the of Uniprot reference proteomes (July 2017). Using this similarity information, we taxonomically annotated the scaffolds with blobtools using parameters “-x bestsumorder --rank phylum”.
DOI: 10.6084/m9.figshare.5688952.v1
title: Appendix 3-figure 3: Ilumi1.0 Blobtools results

description: We sought to systematically remove assembled non-elaterid contaminant sequence from Ilumi1.0. Using the blobtools toolset (v.1.0.1), we taxonomically annotated our scaffolds by performing a blastn (v2.6.0+) nucleotide sequence similarity search against the NCBI nt database, and a diamond (v.0.9.10.111) translated nucleotide sequence similarity search against the of Uniprot reference proteomes (July 2017). Using this similarity information, we taxonomically annotated the scaffolds with blobtools using parameters “-x bestsumorder --rank phylum”.
DOI: 10.6084/m9.figshare.5688949
title: A new phylogeny of ichthyosaurs (Reptilia: Diapsida)

description: The largest phylogenetic analysis of ichthyosaurs to date is presented, with 114 ingroup taxa coded at species level. Completeness of the taxa included varied from &gt; 98% to &lt; 2%; 10 taxa were removed <i>a priori</i> using Concatabominations due to incompleteness and taxonomic uncertainty. The data were analysed using three widely used optimization criteria, maximum parsimony, maximum likelihood and Bayesian inference; while similar, each criterion produced different topologies, support and levels of resolution. Maximum parsimony found a poorly-resolved consensus tree with moderate improvement from <i>a posteriori</i> pruning of unstable taxa; however, general support remained low. Tree resolution was reduced more by taxa that lacked codings from phylogenetically important regions of the tree, rather than by those that simply lacked many codings. Resolution present in the most likely tree is poorly supported; sister relationships cannot be confirmed, although similarities are found to the most parsimonious tree. Bayesian inference found poorly resolved consensus trees. While more resolved, an equal-distribution rate prior is significantly worse than the null gamma-distribution rate prior for morphological data, but suggests rate heterogeneity across ichthyosaur phylogeny. Tree comparisons under each analytical criterion failed to select a single best tree; however, the Bayesian inference tree with gamma-distribution rate prior is selected as the best tree based on recent analyses showing improved accuracy using this criterion. Unequivocally resolved clades include Ichthyopterygia, Ichthyosauria, Shastasauria, Euichthyosauria, Parvipelvia and Neoichthyosauria, but with variation in their taxonomic components. Mixosauridae and Ophthalmosauridae are similarly recovered, but their definitions are modified to stem-based definitions to prevent substantial variation of included taxa. Several genera are not monophyletic: <i>Brachypterygius, Leptonectes, Mixosaurus, Ophthalmosaurus</i>, <i>Paraophthalmosaurus</i>, <i>Phalarodon</i>, <i>Platypterygius</i>, <i>Stenopterygius</i>, <i>Temnodontosaurus</i> and <i>Undorosaurus</i>. Complex and variable relationships suggest the need for new characters and a re-evaluation of the state of ichthyosaur phylogenetics.
DOI: 10.6084/m9.figshare.5688949.v1
title: A new phylogeny of ichthyosaurs (Reptilia: Diapsida)

description: The largest phylogenetic analysis of ichthyosaurs to date is presented, with 114 ingroup taxa coded at species level. Completeness of the taxa included varied from &gt; 98% to &lt; 2%; 10 taxa were removed <i>a priori</i> using Concatabominations due to incompleteness and taxonomic uncertainty. The data were analysed using three widely used optimization criteria, maximum parsimony, maximum likelihood and Bayesian inference; while similar, each criterion produced different topologies, support and levels of resolution. Maximum parsimony found a poorly-resolved consensus tree with moderate improvement from <i>a posteriori</i> pruning of unstable taxa; however, general support remained low. Tree resolution was reduced more by taxa that lacked codings from phylogenetically important regions of the tree, rather than by those that simply lacked many codings. Resolution present in the most likely tree is poorly supported; sister relationships cannot be confirmed, although similarities are found to the most parsimonious tree. Bayesian inference found poorly resolved consensus trees. While more resolved, an equal-distribution rate prior is significantly worse than the null gamma-distribution rate prior for morphological data, but suggests rate heterogeneity across ichthyosaur phylogeny. Tree comparisons under each analytical criterion failed to select a single best tree; however, the Bayesian inference tree with gamma-distribution rate prior is selected as the best tree based on recent analyses showing improved accuracy using this criterion. Unequivocally resolved clades include Ichthyopterygia, Ichthyosauria, Shastasauria, Euichthyosauria, Parvipelvia and Neoichthyosauria, but with variation in their taxonomic components. Mixosauridae and Ophthalmosauridae are similarly recovered, but their definitions are modified to stem-based definitions to prevent substantial variation of included taxa. Several genera are not monophyletic: <i>Brachypterygius, Leptonectes, Mixosaurus, Ophthalmosaurus</i>, <i>Paraophthalmosaurus</i>, <i>Phalarodon</i>, <i>Platypterygius</i>, <i>Stenopterygius</i>, <i>Temnodontosaurus</i> and <i>Undorosaurus</i>. Complex and variable relationships suggest the need for new characters and a re-evaluation of the state of ichthyosaur phylogenetics.
DOI: 10.6084/m9.figshare.5688940
title: A reassessment of the Bovidae (Mammalia) from the Nawata Formation of Lothagam, Kenya, and the late Miocene diversification of the family in Africa

description: The late Miocene Bovidae from the Nawata Formation of Lothagam were all assigned to modern tribes by Harris (2003), with the majority of specimens being referred to a species of <i>Aepyceros</i>, a genus that includes the modern impala. However, an alternative interpretation of the collection lessens the modern character of the faunal composition. Many of the identifications are revised: there might be a single species of Boselaphini, there is no evidence of Hippotragini, and <i>Aepyceros</i> is less common than previously thought. Two new genera, <i>Afrotragus</i> and <i>Turkanatragus</i>, are erected; together with an unnamed species and ‘<i>Kobus</i>’ <i>laticornis</i> Harris, 2003, they cannot easily be allocated to any existing tribe. These two new genera share long, slender, spiralled horn-cores, and it is conceivable that they belong to the same group, which might also include the ‘<i>Prostrepsiceros’</i> from Sahabi, Libya, but does not seem closely related to Eurasian <i>Prostrepsiceros</i>. Along with sparser evidence from elsewhere in Africa, this strongly suggests that by the late Miocene, African Bovidae underwent a wider radiation than reflected in the tribes that survived into the Pliocene, showing that the crown groups very incompletely document the relatively recent past diversity of the family. http://zoobank.org/urn:lsid:zoobank.org:pub:9865FA15-7BFB-4B7E-A01F-714B94351D6D
DOI: 10.6084/m9.figshare.5688940.v1
title: A reassessment of the Bovidae (Mammalia) from the Nawata Formation of Lothagam, Kenya, and the late Miocene diversification of the family in Africa

description: The late Miocene Bovidae from the Nawata Formation of Lothagam were all assigned to modern tribes by Harris (2003), with the majority of specimens being referred to a species of <i>Aepyceros</i>, a genus that includes the modern impala. However, an alternative interpretation of the collection lessens the modern character of the faunal composition. Many of the identifications are revised: there might be a single species of Boselaphini, there is no evidence of Hippotragini, and <i>Aepyceros</i> is less common than previously thought. Two new genera, <i>Afrotragus</i> and <i>Turkanatragus</i>, are erected; together with an unnamed species and ‘<i>Kobus</i>’ <i>laticornis</i> Harris, 2003, they cannot easily be allocated to any existing tribe. These two new genera share long, slender, spiralled horn-cores, and it is conceivable that they belong to the same group, which might also include the ‘<i>Prostrepsiceros’</i> from Sahabi, Libya, but does not seem closely related to Eurasian <i>Prostrepsiceros</i>. Along with sparser evidence from elsewhere in Africa, this strongly suggests that by the late Miocene, African Bovidae underwent a wider radiation than reflected in the tribes that survived into the Pliocene, showing that the crown groups very incompletely document the relatively recent past diversity of the family. http://zoobank.org/urn:lsid:zoobank.org:pub:9865FA15-7BFB-4B7E-A01F-714B94351D6D
DOI: 10.6084/m9.figshare.5688928
title: Appendix 2-figure 2: Alat1.2 Blobtools results

description: Potential contaminants in Alat1.2 were identified using the blobtools toolset (v.1.0). First, scaffolds were compared to known sequences by performing a blastn (v2.5.0+) nucleotide sequence similarity search against the NCBI nt database and a diamond (v.0.9.10) translated nucleotide sequence similarity search against the of Uniprot reference proteomes (July 2017). Using this similarity information, scaffolds were annotated with blobtools (parameters “-x bestsumorder”). We also inspected the read coverage by mapping the paired-end reads (FFGPE_PE200) on the genome using bowtie2. The contigs derived from potential contaminants and/or poor quality contigs were then removed: contigs with higher %GC (&gt;50%) with bacterial hits or no database hits and showing low read coverage (&lt;30x) (see Supplementary Figure 2.5.1.1). This process removed 1925 scaffolds (1.17 Mbp), representing 26.3% of the scaffold number and 1.3% of the nucleotides of Alat1.2, producing the final filtered assembly, dubbed Alat1.3.
DOI: 10.6084/m9.figshare.5688922
title: FLO1K - Minimum Annual Flow Time Series 1960-2015

description: NetCDF metadata:<br> netcdf FLO1K.ts.1960.2015.qmi {<br> dimensions:<br> time = UNLIMITED ; // (56 currently)<br> lat = 21600 ;<br> lon = 43200 ;<br> variables:<br> double lat(lat) ;<br> lat:standard_name = "latitude" ;<br> lat:long_name = "latitude" ;<br> lat:units = "degrees_north" ;<br> double lon(lon) ;<br> lon:standard_name = "longitude" ;<br> lon:long_name = "longitude" ;<br> lon:units = "degrees_east" ;<br> float qmi(time, lat, lon) ;<br> qmi:_FillValue = -1.f ;<br> qmi:grid_mapping = "crs" ;<br> qmi:long_name = "minimum annual streamflow" ;<br> qmi:description = "minimum mean monthly streamflow of the year" ;<br> qmi:units = "m3/s" ;<br> float time(time) ;<br> time:units = "days since 1900-01-01 00:00:00" ;<br> time:standard_name = "time" ;<br> time:calendar = "gregorian" ;<br> int crs ;<br> crs:long_name = "Lon/Lat Coords in WGS84" ;<br> crs:grid_mapping_name = "latitude_longitude" ;<br> crs:longitude_of_prime_meridian = 0. ;<br> crs:semi_major_axis = 6378137. ;<br> crs:inverse_flattening = 298.257223563 ;<br> <br> // global attributes:<br> :Conventions = "CF-1.6" ;<br> :title = "FLO1K: global maps of mean, maximum and minimum annual streamflow at 1 km resolution from 1960 through 2015" ;<br> :institution = "Radboud University & PBL Netherlands Environmental Assessment Agency" ;<br> :source = "FLO1K v1.0" ;<br> :scenario = "Historical run 1960-2015, yearly timesteps" ;<br> :comment = "" ;<br> :references = "For documentation, see Barbarossa et al. (Sci. Data, 2018)" ;<br> :disclaimer = "This data was produced with the utmost care, based on methods described in the above article. Please cite the above article when using any part of this data in your work." ;<br> :history = "Created on 2017-12-07" ;<br> }
DOI: 10.6084/m9.figshare.5688928.v1
title: Appendix 2-figure 2: Alat1.2 Blobtools results

description: Potential contaminants in Alat1.2 were identified using the blobtools toolset (v.1.0). First, scaffolds were compared to known sequences by performing a blastn (v2.5.0+) nucleotide sequence similarity search against the NCBI nt database and a diamond (v.0.9.10) translated nucleotide sequence similarity search against the of Uniprot reference proteomes (July 2017). Using this similarity information, scaffolds were annotated with blobtools (parameters “-x bestsumorder”). We also inspected the read coverage by mapping the paired-end reads (FFGPE_PE200) on the genome using bowtie2. The contigs derived from potential contaminants and/or poor quality contigs were then removed: contigs with higher %GC (&gt;50%) with bacterial hits or no database hits and showing low read coverage (&lt;30x) (see Supplementary Figure 2.5.1.1). This process removed 1925 scaffolds (1.17 Mbp), representing 26.3% of the scaffold number and 1.3% of the nucleotides of Alat1.2, producing the final filtered assembly, dubbed Alat1.3.
DOI: 10.6084/m9.figshare.5688922.v1
title: FLO1K - Minimum Annual Flow Time Series 1960-2015

description: NetCDF metadata:<br> netcdf FLO1K.ts.1960.2015.qmi {<br> dimensions:<br> time = UNLIMITED ; // (56 currently)<br> lat = 21600 ;<br> lon = 43200 ;<br> variables:<br> double lat(lat) ;<br> lat:standard_name = "latitude" ;<br> lat:long_name = "latitude" ;<br> lat:units = "degrees_north" ;<br> double lon(lon) ;<br> lon:standard_name = "longitude" ;<br> lon:long_name = "longitude" ;<br> lon:units = "degrees_east" ;<br> float qmi(time, lat, lon) ;<br> qmi:_FillValue = -1.f ;<br> qmi:grid_mapping = "crs" ;<br> qmi:long_name = "minimum annual streamflow" ;<br> qmi:description = "minimum mean monthly streamflow of the year" ;<br> qmi:units = "m3/s" ;<br> float time(time) ;<br> time:units = "days since 1900-01-01 00:00:00" ;<br> time:standard_name = "time" ;<br> time:calendar = "gregorian" ;<br> int crs ;<br> crs:long_name = "Lon/Lat Coords in WGS84" ;<br> crs:grid_mapping_name = "latitude_longitude" ;<br> crs:longitude_of_prime_meridian = 0. ;<br> crs:semi_major_axis = 6378137. ;<br> crs:inverse_flattening = 298.257223563 ;<br> <br> // global attributes:<br> :Conventions = "CF-1.6" ;<br> :title = "FLO1K: global maps of mean, maximum and minimum annual streamflow at 1 km resolution from 1960 through 2015" ;<br> :institution = "Radboud University & PBL Netherlands Environmental Assessment Agency" ;<br> :source = "FLO1K v1.0" ;<br> :scenario = "Historical run 1960-2015, yearly timesteps" ;<br> :comment = "" ;<br> :references = "For documentation, see Barbarossa et al. (Sci. Data, 2018)" ;<br> :disclaimer = "This data was produced with the utmost care, based on methods described in the above article. Please cite the above article when using any part of this data in your work." ;<br> :history = "Created on 2017-12-07" ;<br> }
DOI: 10.6084/m9.figshare.5688919
title: FLO1K - Maximum Annual Flow Time Series 1960-2015

description: NetCDF metadata:<br> netcdf FLO1K.ts.1960.2015.qma {<br> dimensions:<br> time = UNLIMITED ; // (56 currently)<br> lat = 21600 ;<br> lon = 43200 ;<br> variables:<br> double lat(lat) ;<br> lat:standard_name = "latitude" ;<br> lat:long_name = "latitude" ;<br> lat:units = "degrees_north" ;<br> double lon(lon) ;<br> lon:standard_name = "longitude" ;<br> lon:long_name = "longitude" ;<br> lon:units = "degrees_east" ;<br> float qma(time, lat, lon) ;<br> qma:_FillValue = -1.f ;<br> qma:grid_mapping = "crs" ;<br> qma:long_name = "maximum annual streamflow" ;<br> qma:description = "maximum mean monthly streamflow of the year" ;<br> qma:units = "m3/s" ;<br> float time(time) ;<br> time:units = "days since 1900-01-01 00:00:00" ;<br> time:standard_name = "time" ;<br> time:calendar = "gregorian" ;<br> int crs ;<br> crs:long_name = "Lon/Lat Coords in WGS84" ;<br> crs:grid_mapping_name = "latitude_longitude" ;<br> crs:longitude_of_prime_meridian = 0. ;<br> crs:semi_major_axis = 6378137. ;<br> crs:inverse_flattening = 298.257223563 ;<br> <br> // global attributes:<br> :Conventions = "CF-1.6" ;<br> :title = "FLO1K: global maps of mean, maximum and minimum annual streamflow at 1 km resolution from 1960 through 2015" ;<br> :institution = "Radboud University & PBL Netherlands Environmental Assessment Agency" ;<br> :source = "FLO1K v1.0" ;<br> :scenario = "Historical run 1960-2015, yearly timesteps" ;<br> :comment = "" ;<br> :references = "For documentation, see Barbarossa et al. (Sci. Data, 2018)" ;<br> :disclaimer = "This data was produced with the utmost care, based on methods described in the above article. Please cite the above article when using any part of this data in your work." ;<br> :history = "Created on 2017-12-07" ;<br> }