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19 results for “Trove”
trove-newspaper-issues
<p>This dataset contains information about the published issues of newspapers digitised and made available through Trove. The data was harvested from the Trove API, using <a href="https://glam-workbench.net/trove-newspapers/harvest_newspaper_issues/">this notebook in the GLAM Workbench</a>.</p> <p>There are two data files:</p> <ul> <li><code>newspaper_issues_totals_by_year.csv</code> – the total number of newspaper issues per year for each digitised newspaper</li> <li><code>newspaper_issues.csv</code> – a complete list of newspaper issues available from Trove</li> </ul> <h2>newspaper_issues_totals_by_year.csv</h2> <p>The dataset contains the following columns:</p> <table> <tbody> <tr> <td><strong>Column</strong></td> <td><strong>Contents</strong></td> </tr> <tr> <td><code>title</code></td> <td>newspaper title</td> </tr> <tr> <td><code>title_id</code></td> <td>newspaper id</td> </tr> <tr> <td><code>state</code></td> <td>place of publication</td> </tr> <tr> <td><code>year</code></td> <td>year published</td> </tr> <tr> <td><code>issues</code></td> <td>number of issues</td> </tr> </tbody> </table> <h2>newspaper_issues.csv</h2> <p>The dataset contains the following columns:</p> <table> <tbody> <tr> <td><strong>Column</strong></td> <td><strong>Contents</strong></td> </tr> <tr> <td><code>title</code></td> <td>newspaper title</td> </tr> <tr> <td><code>title_id</code></td> <td>newspaper id</td> </tr> <tr> <td><code>state</code></td> <td>place of publication</td> </tr> <tr> <td><code>issue_id</code></td> <td>issue identifier</td> </tr> <tr> <td><code>issue_date</code></td> <td>date of publication (YYYY-MM-DD)</td> </tr> </tbody> </table> <p>To keep the file size down, I haven't included an <code>issue_url</code> in this dataset, but these are easily generated from the <code>issue_id</code>. Just add the <code>issue_id</code> to the end of <code>http://nla.gov.au/nla.news-issue</code>. For example: <a href="http://nla.gov.au/nla.news-issue495426">http://nla.gov.au/nla.news-issue495426</a>. Note that when you follow an issue url, you actually get redirected to the url of the first page in the issue.</p>
Trove tag counts
<p>This dataset was derived from the full harvest of <a href="../doi/10.5281/zenodo.5094313">Trove public tags</a>. It contains a list of unique tags and the total number of resources in Trove each tag is attached to. It is formatted as a CSV file with the following columns:</p> <ul> <li>`tag` – the tag string</li> <li>`count` – number of resources the tag has been applied to</li> </ul> <p>User content added to Trove, including tags, is available for reuse under a CC-BY-NC-SA licence.</p>
Determining Antioxidant Activity of Cannabis Leaves Extracts from Different Varieties—Unveiling Nature's Treasure Trove
<p>Article, Dataset for article</p> <p> </p> <h1>Determining Antioxidant Activity of Cannabis Leaves Extracts from Different Varieties—Unveiling Nature’s Treasure Trove</h1> <p> </p> <h2>Abstract</h2> <div>Cannabis leaves contain a diverse range of antioxidants, including cannabinoids, flavonoids, and phenolic compounds, which offer significant health benefits. Utilising cannabis leaves as a source of antioxidants presents a cost-effective approach because they are typically discarded during the cultivation of cannabis plants for their seeds or fibres. Therefore, this presented study aimed to assess the antioxidant activity of the leaves of selected hemp cultivars, such as Białobrzeska, Tygra, and Henola, based on the results obtained with the 2,2′-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid, ferric reducing antioxidant power, cupric reducing antioxidant capacity, and 2,2-Diphenyl-1-picrylhydrazyl assays. The cannabinoid profile was analysed for the antioxidant activity to the contents of cannabidiol (CBD), cannabigerol (CBG), Δ<sup>9</sup>-tetrahydrocannabinol (Δ<sup>9</sup>-THC), and cannabichromene (CBC), determined based on chromatographic assays. The following variables were tested: the impact of various extractants (methanol, ethanol, and isopropanol), and their mixtures (50:50, <span>v/v</span>, as well as extraction methods (maceration and ultra-sound-assisted extraction) significant in obtaining hemp extracts characterised by different cannabinoid profiles. The results revealed that the selection of extractant and extraction conditions significantly influenced the active compounds’ extraction efficiency and antioxidant activity. Among the tested conditions, ultrasound-assisted extraction using methanol yielded the highest cannabinoid profile: CBD = 184.51 ± 5.61; CBG = 6.10 ± 0.21; Δ9-THC = 0.51 ± 0.01; and CBC = 0.71 ± 0.01 μg/g antioxidant potential in Białobrzeska leaf extracts.</div> <div> <div> <div>Keywords: </div> <a href="https://www.mdpi.com/search?q=Cannabis+sativa"><span>Cannabis sativa</span></a>; <a href="https://www.mdpi.com/search?q=antioxidant">antioxidant</a>; <a href="https://www.mdpi.com/search?q=cannabidiol">cannabidiol</a>; <a href="https://www.mdpi.com/search?q=cannabigerol">cannabigerol</a>; <a href="https://www.mdpi.com/search?q=oxidative+stress">oxidative stress</a></div> </div>
Public tags added to resources in Trove, 2008 to 2024
<p>This dataset contains details of 2,495,958 unique public tags added to 10,403,650 resources in <a href="https://trove.nla.gov.au/">Trove</a> between August 2008 and June 2024. I harvested the data using the Trove API and saved it as a CSV file with the following columns:</p> <ul> <li>`tag` – lower-cased text tag</li> <li>`date` – date the tag was added</li> <li>`zone` – API zone containing the tagged resource</li> <li>`record_id` – the identifier of the tagged resource</li> </ul> <p>I've documented the method used to harvest the tags in <a href="https://github.com/GLAM-Workbench/trove-lists/blob/master/harvest-tags.ipynb">this notebook</a>.</p> <p>Using the `zone` and `record_id` you can find more information about a tagged item. To create urls to the resources in Trove:</p> <ul> <li>for resources in the 'book', 'article', 'picture', 'music', 'map', and 'collection' zones add the `record_id` to `https://trove.nla.gov.au/work/`</li> <li>for resources in the 'newspaper' and 'gazette' zones add the `record_id` to `https://trove.nla.gov.au/article/`</li> <li>for resources in the 'list' zone add the `record_id` to `https://trove.nla.gov.au/list/`</li> </ul> <p>Notes:</p> <ul> <li>Works (such as books) in Trove can have tags attached at either work or version level. This dataset aggregates all tags at the work level, removing any duplicates.</li> <li>A single resource in Trove can appear in multiple zones – for example, a book that includes maps and illustrations might appear in the 'book', 'picture', and 'map' zones. This means that some of the tags will essentially be duplicates – harvested from different zones, but relating to the same resource. Depending on your needs, you might want to remove these duplicates.</li> <li>While most of the tags were added by Trove users, more than 500,000 tags were added by Trove itself in November 2009. I think these tags were automatically generated from related Wikipedia pages. Depending on your needs, you might want to exclude these by limiting the date range or zones.</li> <li>User content added to Trove, including tags, is available for reuse under a CC-BY-NC licence.</li> </ul> <p>See <a href="https://github.com/GLAM-Workbench/trove-lists/blob/master/analyse_tags.ipynb">this notebook</a> for some examples of how you can manipulate, analyse, and visualise the tag data.</p>
Trove of Gut Virus Genomes (TGVG)
<p> </p> <p><strong>TGVG_v1.1.genomes.all.fna</strong></p> <p>Sequences from the Gut Virome Database, the Cenote Human Virome Database, the Metagenomic Gut Virus catalog, and the Gut Phage Database were downloaded and dereplicated at 95% average nucleotide identity (ANI) across 85% alignment fraction (AF) using anicalc.py and aniclust.py from the CheckV (version 0.9.0) package, in line with metagenomic virus sequence community standards. Exemplar sequences from each cluster/singleton from the input sequences were kept and ran through Cenote-Taker 2 (version 2.1.5) to predict virus hallmark genes within each sequence using the ‘virion’ hallmark gene database. Sequences were kept if they 1) encoded direct terminal repeats (signature of complete virus genome), one or more virus hallmark genes, and were over 1.5 kilobases or longer, or 2) encoded 2 or more virus hallmark genes and were over 12 kilobases. Sequences passing this threshold were run through CheckV to remove flanking host (bacterial) sequences and quantify the virus gene/bacteria gene ratio for each contig. Sequences with 3 or fewer virus genes and 3 or more bacterial genes after pruning/were discarded. Finally, sequences passing this threshold were dereplicated again with CheckV scripts at 95% ANI and 85% AF to yield the Trove of Gut Virus Genomes of 110,296 genomes/genome fragments each representing a viral SGB.</p> <p> </p> <p><strong>TGVG_v1.1_metadata.tsv</strong></p> <p>For each sequence in the Trove of Gut Virus Genomes CheckV was used to estimate completeness, ipHOP (version 1.1.0) was used to predict bacterial/archael host genus. Bacphlip (version 0.9.3) was run on each of the sequences predicted to be 90% or more complete to predict phage virulence.<br> vConTACT2 (version 0.11.3) was used to cluster viral SGBs from the Trove of Gut Virus Genomes into virus clusters. In addition to viral SGBs with vConTACT2 “Singleton” labels, viral SGBs with vConTACT2 labels “Unassigned”, “Outlier”, “Overlap”, “Clustered/Singleton” were also considered “Singletons” for downstream analysis. Genomad (version 1.5.2) taxonomy module was run on each sequence to obtain taxonomical assignment at the phylum, class, order, and family levels.<br> </p>
Fig. 11 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 11. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia madrensis (holotype worker), S. JTL066 (worker, CASENT0610648), S. benevidesae (holotype worker), S. chiapaneca (holotype worker), S. parietalis (holotype worker), S. setosa (holotype worker), S. JTL073 (worker, MCZ-ENT00511569), S. JTL075 (worker, CASENT0601445), S. disjuncta (holotype worker), and S. augustae (worker, CASENT0644275). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Fig. 10 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 10. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia jennierussae (holotype worker), S. persimilis (holotype worker), S. JTL018 (worker, JTLC000013995), S. machaquila (holotype worker), S. murillocruzae (holotype worker), S. truncata (holotype worker), S. JTL084 (worker, FMNHINS0000095760), S. JTL050 (worker, CASENT0249320), S. JTL082 (worker, CASENT0617700), and S. honduriana (lectotype worker). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Fig. 7 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 7. Phylogenetic relationships among COI barcode sequences for Syscia. Red samples were sequenced for UCEs. Black samples were downloaded from the BOLD database.The tree was inferred using IQ-TREE with the data partitioned by codon position. Black circles on nodes indicate high support, which we define as ≥95% ultrafast bootstrap support and ≥95% SH-like branch support. Clades of named species are shaded as a visual aid, with gray outlines indicating non-monophyly of species.
Fig. 1 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 1. Variation in Syscia occipital carina. (A) Flange weakly developed, less visible in face view. (B) Flange strongly developed, easily visible in face view.
Fig. 6 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 6. Phylogeny of New World Syscia, inferred using the program IQ-TREE and 1,388 UCE loci.Two outgroup taxa (two species of Ooceraea) are not shown. Node support values (ultrafast bootstrap/SH-like) <100/100 are depicted with red dots.The imaged specimen is S. ticomontana (CASENT0644376).
Fig. 3 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 3. Variation in Syscia profiles and pilosity. (A) AIII in dorsal view trapezoidal, with convex sides. (B) AIII in dorsal view weakly trapezoidal, with convex sides. (C) AIII in dorsal view trapezoidal, with flat sides. (D) AIV in dorsal view, with convex sides, anterior margin not truncate. (E) AIV in dorsal view, with convex sides, anterior margin moderately truncate. (F) AIV in dorsal view, with nearly flat sides, anterior margin strongly truncate. (G) AIII dorsal profile strongly convex. (H) AIII dorsal profile weakly convex. (I) AIII dorsal profile flat. (J) AIV dorsal profile convex. (K) AIV dorsal profile weakly convex. (L) AIV dorsal profile flat. (A, B, G, J) Standing pilosity long, coarse. (C, H, K) Standing pilosity of medium length and thickness. (I, L) Standing pilosity short, fine.
Fig. 13 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 13. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia latepunctata (holotype worker), S. borowieci (holotype worker), S. volucris (holotype worker), S. JTL076 (queen, CASENT0614221),S. JTL064 (worker, CASENT0631661), S. JTL033 (worker, CASENT0611831),S. grandis (holotype worker), and S. JTL003 (worker, INB0003213589). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Fig. 9 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 9. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia pervagata (holotype worker), S. peten (holotype worker), S. JTL074 (worker, MCZ-ENT00511564), S. brachyptera (holotype worker), S. valenzuelai (holotype worker), S. JTL071 (worker, FMNHINS0000095759), S. quisquillis (holotype worker), S. sumnichti (holotype worker), S. JTL060 (worker, CASENT0644220), and S. JTL085 (worker, CASENT0602939). Scale bars 0.2 mm. Species are in order of mean HW, which is shown in the lower left of the distribution map. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Fig. 2 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 2. Variation in Syscia subpetiolar process. (A) Subtriangular with flat to concave posterior margin. (B) Subtriangular with convex posterior margin. (C) Subtriangular with small tooth on posterior margin. (D) Subquadrate. (E) Subtriangular with large acute tooth on posterior margin. F. With fenestra and notch on posterior margin.
Fig. 4 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 4. Illustrations of Syscia measurements. HL: head length, HW: head width, MSL: mesosoma length, AIIIL: abdominal tergite III length, AIIIW: abdominal tergite III width, AIVL: abdominal tergite IV length, AIIVW: abdominal tergite IV width.
Fig. 12 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 12. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia tolteca (lectotype worker), S. atitlana (holotype worker), S. lacandona (holotype worker), S. JTL049 (worker, CASENT0644222), S. JTL065 (worker, CASENT0602939), S. amblyogyna (holotype worker), S. ticomontana (holotype worker), S. JTL017 (worker, INB0003693097), S. JTL079 (worker, CASENT0642985), and S. transisthmica (holotype worker). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.2 mm. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality (not shown for S. tolteca, with type locality 'Guatemala').
Fig. 8 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 8. Distribution map, face view, lateral view of petiole-AIV, and dorsal view of AIII-AIV of Syscia minuta (holotype worker), S. parva (holotype worker), S. JTL067 (worker, CASENT0644012), S. pollula (holotype worker), S. JTL069 (worker, CASENT0644008), S. JTL068 (queen, CASENT0613276), S. austrella (holotype worker), S. JTL037 (worker, CASENT0635747), S. quisquillis Arizona form (worker, FMNHINS0000095772), and S. boudinoti (holotype worker). Species are in order of mean HW, which is shown in the lower left of the distribution map. Scale bars 0.1 mm for S. minuta to S. JTL037, 0.2 mm for S. quisquillis Arizona form and S. boudinoti. On distribution maps, red dots are sites with UCE sequence data. Red boxes are type locality.
Integrating UCE phylogenomics with traditional taxonomy reveals a trove of New World Syscia species (Formicidae, Dorylinae)
<p>The ant genus <em>Syscia</em> is part of the cryptic ant fauna inhabiting leaf litter and rotten wood in the Asian and American tropics. It is a distinct clade within the Dorylinae, the subfamily from which army ants arose. Prior to this work the genus comprised seven species, each known from a single or very few collections. Extensive collecting in Middle America revealed an unexpected and challenging diversity of morphological forms. Locally distinct forms could be identified at many sites but assignment of specimens to species spanning multiple sites was problematic. To improve species delimitation, Ultra-Conserved Element (UCE) phylogenomic data were sequenced for all forms, both within and among sites, and a phylogeny was inferred. Informed by phylogeny, species delimitation was based on monophyly, absence of within-clade sympatry, and a subjective degree of morphological uniformity. UCE phylogenomic results for 130 specimens were complemented by analysis of mitochondrial COI (DNA barcode) data for an expanded taxon set. The resulting taxonomy augments the number of known species in the New World from 3 to 57. We describe and name 31 new species, and 23 species are assigned morphospecies codes pending improved specimen coverage. Queens may be fully alate or brachypterous, and there is a wide variety of intercaste female forms. Identification based on morphology alone is very difficult due to continuous character variation and high similarity of phylogenetically distant species. An identification aid is provided in the form of a set of distribution maps and standard views, with species ordered by size.</p>
Fig. 5 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)
Fig. 5. Mesosomal structure of fully alate (A) vs. brachypterous (B) queen.
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