229 research outputs found
Research applications of primary biodiversity databases in the digital age.
Our world is in the midst of unprecedented change-climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed. We found that the most common uses of online biodiversity databases have been to estimate species distribution and richness, to outline data compilation and publication, and to assist in developing species checklists or describing new species. Only 69% of papers in our dataset addressed one or more aspects of data quality, which is low considering common errors and biases known to exist in opportunistic datasets. Globally, we find that biodiversity databases are still in the initial stages of data compilation. Novel and integrative applications are restricted to certain taxonomic groups and regions with higher numbers of quality records. Continued data digitization, publication, enhancement, and quality control efforts are necessary to make biodiversity science more efficient and relevant in our fast-changing environment
Research applications of primary biodiversity databases in the digital age
Our world is in the midst of unprecedented change-climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed
Constructing Delaunay triangulations along space-filling curves
Incremental construction con BRIO using a space-filling curve order for insertion is a popular algorithm for constructing Delaunay triangulations. So far, it has only been analyzed for the case that a worst-case optimal point location data structure is used which is often avoided in implementations. In this paper, we analyze its running time for the more typical case that points are located by walking. We show that in the worst-case the algorithm needs quadratic time, but that this can only happen in degenerate cases. We show that the algorithm runs in O(n logn) time under realistic assumptions. Furthermore, we show that it runs in expected linear time for many random point distributions. This research was supported by the Deutsche Forschungsgemeinschaft within the European graduate program ’Combinatorics, Geometry, and Computation’ (No. GRK 588/2) and by the Netherlands’ Organisation for Scientific Research (NWO) under BRICKS/FOCUS grant number 642.065.503 and project no. 639.022.707
The disruption of GDP-fucose de novo biosynthesis suggests the presence of a novel fucose-containing glycoconjugate in <i>Plasmodium</i> asexual blood stages
Glycosylation is an important posttranslational protein
modification in all eukaryotes. Besides
glycosylphosphatidylinositol (GPI) anchors and N-glycosylation,
O-fucosylation has been recently reported in key sporozoite
proteins of the malaria parasite. Previous analyses showed the
presence of GDP-fucose (GDP-Fuc), the precursor for all
fucosylation reactions, in the blood stages of Plasmodium
falciparum. The GDP-Fuc de novo pathway, which requires the
action of GDP-mannose 4,6-dehydratase (GMD) and GDP-L-fucose
synthase (FS), is conserved in the parasite genome, but the
importance of fucose metabolism for the parasite is unknown. To
functionally characterize the pathway we generated a PfGMD
mutant and analyzed its phenotype. Although the labelling by the
fucose-binding Ulex europaeus agglutinin I (UEA-I) was
completely abrogated, GDP-Fuc was still detected in the mutant.
This unexpected result suggests the presence of an alternative
mechanism for maintaining GDP-Fuc in the parasite. Furthermore,
PfGMD null mutant exhibited normal growth and invasion rates,
revealing that the GDP-Fuc de novo metabolic pathway is not
essential for the development in culture of the malaria parasite
during the asexual blood stages. Nonetheless, the function of
this metabolic route and the GDP-Fuc pool that is generated
during this stage may be important for gametocytogenesis and
sporogonic development in the mosquito
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