1,720,954 research outputs found
Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads
No full textThe implementation of Hi-C reads in the de novo genome assembly process allows the ordering of large regions of the genome in scaffolds and the generation of chromosome-level assemblies. Several bioinformatics tools have been developed for genome scaffolding with Hi-C, and each tool has advantages and disadvantages that need to be carefully evaluated before their adoption. We generated two de novo assemblies of Arabidopsis thaliana obtained from the same raw PacBio HiFi and Oxford Nanopore Technologies data. We scaffolded the assemblies implementing Hi-C reads with the scaffolders 3D-DNA, SALSA2, and YaHS, with the aim of identifying the tool providing the most accurate assembly. The scaffolded assemblies were evaluated according to contiguity, completeness, accuracy, and structural correctness. In our analysis, YaHS proved to be the best-performing bioinformatics tool for scaffolding de novo genome assemblies in Arabidopsis thaliana
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Valuable non-food crops for biochar-assisted phytoremediation of contaminated soils: The case of cardoon, rapeseed and safflower
No full textBiochar can affect the bioavailability of potentially toxic elements (PTEs) in contaminated soils thereby influencing plant growth. For this reason, biochar could be a resource for the assisted phytostabilisation of PTEs-polluted soils. The aim of this study was therefore to assess the influence of a softwood-derived biochar (5 % w/w), added to soils (S1 and S2) contaminated with Cd (4.8 and 74 mg·kg−1), Pb (318 and 1899 mg·kg−1) and Zn (622 and 3803 mg·kg−1), on selected soil biochemical and microbial features. The suitability of biochar in the assisted phytostabilisation in combination with cardoon, rapeseed and safflower was also evaluated. Overall, biochar decreased (or left unaffected) the number of culturable bacteria, actinomycetes and fungi in both soils. Soil enzyme activities were also reduced by biochar (e.g., −64 and 75 % for dehydrogenase and −16 % and 22 % for β-glucosidase in S1- and S2 + Bio), while urease activity increased (+190 and 46 % in S1- and S2 + Bio). Actinobacteria and bacterial taxa involved in soil nitrogen cycling (e.g., Nitrospira) were enriched in biochar-amended soils, while a marked loss of Cyanobacteria and taxa associated with oligotrophic conditions (e.g. Gaiellales, Sericithochromatia, Methylinbuim, Solimonadaceae, Gammaprotobacteriaceae and Salinisphaerales) was recorded. Increased root biomass of cardoon (+22 and 14 % in S1- and S2 + Bio compared to control plants), safflower (+71 and 98 % in S1- and S2 + Bio), and rapeseed (+17.1 + 2.4 % in S1- and S2 + Bio) was recorded in the amended soils. An increase of safflower and rapeseed shoots was also detected. In most cases, biochar addition reduced the PTEs concentration in plant roots/shoots/seeds favouring their build up (as total amounts) in the roots, as a consequence of enhanced growth due to biochar. Overall, the results indicated that safflower, rapeseed and cardoon can be used in assisted phytoremediation programmes of PTEs-contaminated soils, providing some valuable biomass that can generate income
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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