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  • 1
    Publication Date: 2008-03-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cochard, Roland -- Agosti, Donat -- New York, N.Y. -- Science. 2008 Mar 28;319(5871):1759-61; author reply 1759-61. doi: 10.1126/science.319.5871.1759d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18369124" target="_blank"〉PubMed〈/a〉
    Keywords: *Acacia/growth & development ; Animals ; *Ants/physiology ; Cattle ; *Ecosystem ; *Fires ; *Symbiosis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2024-01-12
    Description: A vast amount of biodiversity data is reported in the primary taxonomic literature. In the past, we have demonstrated the use of semantic enhancement to extract data from taxonomic literature and make it available to a network of databases (Miller et al. 2015). For technical reasons, semantic enhancement of taxonomic literature is most efficient when customized according to the format of a particular journal. This journal-based approach captures and disseminates data on whatever taxa happen to be published therein. But if we want to extract all treatments on a particular taxon of interest, these are likely to be spread across multiple journals. Fortunately, the GoldenGATE Imagine document editor (Sautter 2019) is flexible enough to parse most taxonomic literature. \nTyrannosaurus rex is an iconic dinosaur with broad public appeal, as well as the subject of more than a century of scholarship. The Naturalis Biodiversity Center recently acquired a specimen that has become a major attraction in the public exhibit space. For most species on earth, the primary taxonomic literature contains nearly everything that is known about it. Every described species on earth is the subject of one or more taxonomic treatments. A taxon-based approach to semantic enhancement can mobilize all this knowledge using the network of databases and resources that comprise the modern biodiversity informatics infrastructure. When a particular species is of special interest, a taxon-based approach to semantic enhancement can be a powerful tool for scholarship and communication. In light of this, we resolved to semantically enhance all taxonomic treatments on T. rex. Our objective was to make these treatments and associated data available for the broad range of stakeholders who might have an interest in this animal, including professional paleontologists, the curious public, and museum exhibits and public communications personnel. Among the routine parsing and data sharing activities in the Plazi workflow (Agosti and Egloff 2009), taxonomic treatments, as well as cited figures, are deposited in the Biodiversity Literature Repository (BLR), and occurrence records are shared with the Global Biodiversity Information Facility (GBIF). Treatment citations were enhanced with hyperlinks to the cited treatment on TreatmentBank, and specimen citations were linked to their entries on public facing collections databases. We used the OpenBiodiv biodiversity knowledge graph (Senderov et al. 2017) to discover other taxa mentioned together with T. rex, and to create a timeline of T. rex research to evaluate the impact of individual researchers and specimen repositories to T. rex research. We contributed treatment links to WikiData, and queried WikiData to discover identifiers to different platforms holding data about T. rex. We used bloodhound-tracker.net to disambiguate human agents, like collectors, identifiers, and authors. We evaluate the adequacy of the fields currently available to extract data from taxonomic treatments, and make recommendations for future standards.
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 3
    Publication Date: 2024-04-18
    Description: Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions.
    Keywords: Araneae ; Biodiversity informatics ; Data mining ; Open access ; Spiders ; Taxonomy ; XML ; markup
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 4
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    Pensoft Publishers
    In:  Research Ideas and Outcomes vol. 3 no. e12502
    Publication Date: 2024-04-16
    Keywords: Big data ; Intellectual property rights ; Open Access ; Taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Insectes sociaux 34 (1987), S. 280-290 
    ISSN: 1420-9098
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Description / Table of Contents: Zusammenfassung Maennchen vonFormica exsecta aus zwei Alpentaelern gehoeren zwei verschiedenen Groessenklassen an, Micraner und Macraner genannt. Es wurden Nester mit beiden Groessenklassen, aber auch solche mit nur je einer gefunden. Um zu untersuchen, ob beide Maennchenklassen haploid oder eine diploid war, wurden die Chromosomezahlen in maennlichen Vorpuppen ermittelt und der relative DNA-Wert von einzelnen Gehirnzellen adulter Maennchen bestimmt. Die ueberwiegende Anzahl aller Metaphaseplatten in Gehirnen von Maennchen beider Groessenklassen zeigte die haploide Chromosomenzahl. Der Rest der Metaphasen hatte 2n oder 4n Chromosomensaetze. Arbeiterinnen enthielten ueberwiegend diploide und daneben einige tetraploide Chromosomensaetze im Gehirn. Ein Unterschied zwischen Micranern und Macranern war der Prozentsatz Zellen, die mehr als n Chromosomen hatten. In Macranern waren 90 oder mehr Prozent der Zellen haploid, waehrend in Micranern prozentual weniger haploide Zellen gefunden wurden. Dagegen enthielten nur Micraner Chromosomensaetze mit mehr als 2n. Die DNA-Messungen ergaben aehnliche Resultate. Beide Maennchentypen zeigten den gleichen niedrigen DNA-Wert, niedriger als der der Arbeiterinnen. Uebereinstimmend mit den Chromosomenzaehlungen hatten die Macraner nur eine Klasse hoeherer DNA-Werte. In Macranern wurde zusaetzlich eine Klasse DNA-Werte gefunden, die niedriger, war, als die, welche die n Chromosomenzahl repraesentiert. Diese Werte stammen vermutlich von degenerierenden Kernen. Beide Maennchentypen enthalten Spermien. Die vorliegenden Daten lassen den Schluss zu, dass beiF. exsecta die Maennchengroessenklassen nicht auf einen Haploidie-Diploidie-Mechanismus zurueckzufuehren sind. Einen Unterschied zwischen Micranern und Macranern ergab jedoch die Haeufigkeit endomitotischer Zyklen im Gehirn, also Verdoppellung der Chromosomenzahl ohne anschliessende Zellteilung. In den Gehirnen von Macranern wurden nur Zellen gefunden, die maximal einen endomitotischen Zyklus durchlaufen hatten. Micraner dagegen enthielten Mitosen mit einem vierfachen Choromosomensatz, entstanden durch zwei aufeinander folgende endomitotische Zyklen.
    Notes: Summary Males ofFormica exsecta from two alpine valleys were found to belong to two significantly different size classes, called micraner and macraner. Nests contained either one or the other or both male types. Tot test whether both male types were haploid or one was diploid, chromosome numbers in brain cells from prepupae were counted and the relative DNA value of single nuclei from adult brains was determined. Most of the metaphase plates in brains from micraner as well as from macraner turned out to be haploid. The rest of the metaphases showed a 2n or 4n chromosome set. Workers had diploid brain cells together with some 4n cells. A difference between micraner and macraner was the percentage of cells with more than n chromosomes. All macraner had 90% or more haploid cells in their brain while the percentage of haploid cells in micraner could be much lower, as low as 59%. Only micraner showed chromosome numbers higher than 2n. DNA measurements gave principally the same result. Both male types exhibited the same low DNA value, lower than worker brain cells. In agreement with the chromosome countings, macraner had only one class of cells with a higher DNA value. In addition to the DNA values which are thought to represent the chromosome numbers n and 2n, lower values were found in macraner which are interpreted as degenerating nuclei. Both male types contained sperm. The presented results show that inF. exsecta differences in male size are not induced by a haploid-diploid mechanism. All males were haploid. However, the frequency of endomitotic cycles, the doubling of the chromosome number without subsequent cell division, was lower in macraner than in micraner.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Biochemical Systematics and Ecology 20 (1992), S. 559-572 
    ISSN: 0305-1978
    Keywords: Cataglyphis altisquamis ; Cataglyphis bicolor group ; Cataglyphis cursor group ; Cataglyphis frigidus ; Cataglyphis isis ; Cataglyphis mauritanicus ; Cataglyphis niger ; Cataglyphis nodus ; Cataglyphis ruber ; Dufour gland ; Formicidae ; Hymenoptera ; Insecta ; chemotaxonomy ; mandibular gland
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1423-0445
    Keywords: mandibular glands ; chemotaxonomy ; chirality ; synthesis ; 2-methyl-1-hexanol ; Hymenoptera ; Formicidae ; Formicinae ; Cataglyphis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In all the species of theCataglyphis bicolor group examined yet, i.e.C. bicolor, C. diehli, C. isis, C. nodus, andC. viaticus, 2-methyl-1-hexanol is the characteristic substance and almost the only substance found in the mandibular glands. Its chirality has been determined inC. bicolor and shown to be exclusively (S)-2-methyl-1-hexanol.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1432-1904
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 9
    Publication Date: 2000-11-14
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
    Publication Date: 2018-05-23
    Description: Author(s): A. Agosti, D. Ambrosi, and S. Turzi When living cells are observed at rest on a flat substrate, they can typically exhibit a rounded (symmetric) or an elongated (polarized) shape. Although the cells are apparently at rest, the active stress generated by the molecular motors continuously stretches and drifts the actin network, the cyto... [Phys. Rev. E 97, 052410] Published Tue May 22, 2018
    Keywords: Biological Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
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