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3,172 results for “Publications”
Data from: Reconstructing biological invasions using public surveys: a new approach to retrospectively assess spatio-temporal changes in invasive spread
[No abstract entered]
Public Post Information from Multiple DNS Forums
<p>This dataset contains public post information from popular DNS forums like Cloudflare Community.</p>
Dataset_publication
<p>Dataset analyzed for publication</p>
Data for publication "Probing magnetic orbitals and Berry curvature with circular dichroism in resonant inelastic X-ray scattering"
<p>- plotting scripts for the RIXS spectra presented in the paper</p> <p>- analysis scripts for circular dichroism as function of the electric field</p> <p>- all spectra in HDF5 format</p>
James-S-Santangelo/umc: Updates prior to publication
<ul> <li>Removing unnecessary function definitions and function calls</li> <li>Removing files not longer part of manuscript</li> <li>Fixing typos</li> <li>Updating main README</li> </ul>
Solar cell record device efficiency vs number of cumulative publications since first device published
<p>Solar cell record device efficiency either taken from NREL data, or from the authors publication.</p> <p>Cumulative publications are from the Web of Science after 1974, Scopus for after 1959, and Google scholar before.</p>
Supplementary material 1 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
Details on the fungal genomes/contigs targeted : Data type: Excel spreadsheet
Supplementary material 2 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
The 86 multiple sequence alignments used : Data type: Text
Figure 2 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
Figure 2 - Public fungal ITS sequences are subjected to insufficient trimming in their distal ends. Panel a shows the dissimilarity (y-axis) as a function of the relative sequence position (x-axis). The plot is based on 10,584 sequences from 86 species. Panel b and c show zoom-ins of the 5' and 3' ends, respectively. Dashed lines indicate point-wise standard errors.
Figure 1 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
Figure 1 - Example of poorly trimmed sequences (sequence four and on) from the species Setosphaeria turcica. The 5' end of the alignment is shown, and the poorly trimmed sequences cover the last ~5 bases of SSU and the immediate start of ITS1. The topmost sequence is genome-derived, and sequences two and three are regular Sanger sequences retrieved from the INSDC from other studies than the one with the poorly trimmed sequences (sequences four and on). SeaView v. 4 (Gouy et al. 2010) was used to visualize the alignment.
Figure 3 from: Nilsson RH, Sánchez-García M, Ryberg M, Abarenkov K, Wurzbacher C, Kristiansson E (2017) Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13-24. https://doi.org/10.3897/mycokeys.26.14591
Figure 3 - The proportion of poorly trimmed (y-axis) fungal ITS sequences submitted to the INSDC does not decrease over time (x-axis). The regression line (dashed), which was derived by overdispersed Poisson rate regression, shows a weak but significant increasing trend (yearly relative increase of 0.047, p=0.0291).
Figure 3 from: Abarenkov K, Adams RI, Irinyi L, Agan A, Ambrosio E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra V, Coleine C, Gustafsson C, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M, Svantesson S, Scharn R, Svensson O, Töpel M, Unterseher M, Visagie C, Wurzbacher C, Taylor AFS, Kõljalg U, Schriml L, Nilsson RH (2016) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 16: 1-15. https://doi.org/10.3897/mycokeys.16.10000
Figure 3 - Analysis of the MIxS-BE "building occupancy type" (type of building where the underlying sample was taken).
Figure 2 from: Abarenkov K, Adams RI, Irinyi L, Agan A, Ambrosio E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra V, Coleine C, Gustafsson C, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M, Svantesson S, Scharn R, Svensson O, Töpel M, Unterseher M, Visagie C, Wurzbacher C, Taylor AFS, Kõljalg U, Schriml L, Nilsson RH (2016) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 16: 1-15. https://doi.org/10.3897/mycokeys.16.10000
Figure 2 - Krona chart of the taxonomic affiliation of the BMS sequences down to order level. The Krona chart lists all annotated BMS sequences except those classified as Fungi sp. (36.4%) and those of non-fungal origin (0.9%). An interactive version of the Krona chart is provided as Suppl. material 3. The figure includes pre-existing data plus the data added during the workshop, such that these charts indicate the scientific state of ITS-based Sanger-derived sequencing of the built mycobiome as of spring 2016. Sequences that were not annotated with a single built environment-related term in the INSDC were not included in this effort, and are not represented in these charts.
Figure 1 from: Abarenkov K, Adams RI, Irinyi L, Agan A, Ambrosio E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra V, Coleine C, Gustafsson C, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M, Svantesson S, Scharn R, Svensson O, Töpel M, Unterseher M, Visagie C, Wurzbacher C, Taylor AFS, Kõljalg U, Schriml L, Nilsson RH (2016) Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 16: 1-15. https://doi.org/10.3897/mycokeys.16.10000
Figure 1 - Analysis of the BMS sequences for country of collection. Country centroids marked with bubbles of different size on the global map indicate the number of BMS sequences originating from these countries (54 distinct countries, sequence count ranging from 1 to 2,914). For an additional 2.9% of the sequences, country information could not be restored during the workshop. The figure includes pre-existing data plus the data added during the workshop, such that these charts indicate the scientific state of ITS-based Sanger-derived sequencing of the built mycobiome as of spring 2016. Sequences that were not annotated with a single built environment-related term in the INSDC were not included in this effort, and are not represented in these charts.
iBOL public DNA barcode data in GBIF
<p>Darwin Core Archive for GBIF dataset https://www.gbif.org/dataset/040c5662-da76-4782-a48e-cdea1892d14c Code for generating the dataset is on GitHub https://github.com/rdmpage/gbif-040c5662-da76-4782-a48e-cdea1892d14c</p>
Supplementary material 4 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The interactive Krona chart associated with Figure 2 :
Supplementary material 2 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
The MIxS-BE annotations implemented for the built environment sequences during the workshop :
Figure 3 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
Figure 3 Analysis of the MIxS-BE "building occupancy type" (type of building where the underlying sample was taken). The figure is based on Abarenkov et al. (2016) plus the data added during the workshop, such that it indicates the scientific state of ITS-based Sanger-derived sequencing of the built mycobiome as of spring 2017.
Figure 2 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
Figure 2 Krona chart of the taxonomic affiliation of the built environment sequences down to order level. The Krona chart lists all annotated built environment sequences except those classified as Fungi sp. (32%) and those of non-fungal origin (1%). An interactive version of the Krona chart is provided as Supplementary material 4. The figure is based on Abarenkov et al. (2016) plus the data added during the workshop, such that it indicates the scientific state of ITS-based Sanger-derived sequencing of the built mycobiome as of spring 2017.
Figure 1 from: Nilsson RH, Taylor AFS, Adams RI, Baschien C, Bengtsson-Palme J, Cangren P, Coleine C, Daniel H-M, Glassman SI, Hirooka Y, Irinyi L, Iršėnaitė R, Martin-Sanchez PM, Meyer W, Oh S-Y, Sampaio JP, Seifert KA, Sklenář F, Stubbe D, Suh S-O, Summerbell R, Svantesson S, Unterseher M, Visagie CM, Weiss M, Woudenberg JHC, Wurzbacher C, den Wyngaert SV, Yilmaz N, Yurkov A, Kõljalg U, Abarenkov K (2018) Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65-82. https://doi.org/10.3897/mycokeys.28.20887
Figure 1 Analysis of the built environment sequences for country of collection. Country centroids based on the geographical centres of contiguous country land masses are marked with bubbles of different size on the global map to indicate the number of built environment sequences originating from these countries as stated explicitly in the underlying INSDC records or as restored during the present effort and in Abarenkov et al. (2016) (57 distinct countries, sequence count ranging from 1 to 3,091). The figure is based on Abarenkov et al. (2016) plus the data added during the workshop, such that it indicates the scientific state of ITS-based Sanger-derived sequencing of the built mycobiome as of spring 2017.
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