1,720,963 research outputs found
Element-based graph pangenome
Full text linkGenomic analyses are based on using a single reference genome that does not represent the whole intraspecies diversity. Instead, a pangenome contains the whole genome content of a species. State-of-art models for pangenome representations are divided into linear and nucleotide-based graph pangenomes. The linear model is composed by the reference genome with a set of non-representative reference (NRR) sequences, and it provides information about the presence of a gene in a certain cultivar through presence and absence analysis (PAV analysis). Nucleotide-based graph pangenome allows displaying of local similarities and dissimilarities of genomic regions. In this perspective, the two pangenome models are complementary to each other: the linear pangenome model creates a consensus genome reporting in a table representation the inter-individual gene presence and absence, whereas the nucleotide-based graph pangenome model displays graphically all possible nucleotide variations but cannot be used for gene presence and absence analysis. The aim of this thesis was to create a new pangenome model, called element-based graph pangenome in which it is possible to graphically represent the genes and perform the analysis of the presence and absence of the reported genes. Briefly, genes were annotated in the genomes of 5 different cultivars of Phaseolus vulgaris, through automatic gene prediction. Genes representing nodes in the graph were linked only if they were adjacent in the genome. Then, orthologous genes between different cultivars were identified and merged to represent a single node in the graph. Developed element-based graph pangenome was compared to linear and nucleotide based graph pangenome applied to the same bean accessions. Results showed that due to the merging of gene copies derived by duplication event (paralogs), fewer genes were reported in element-based graph pangenome compared to linear model. Moreover, the visualization of regions was much clearer than that of nucleotide-based graph model, since only the presence or absence of genes across different cultivars was displayed. Different from other pangenome models, element based graph pangenomes provided the advantage of moving information from the gene to the nucleotide in a” zoom-in” visualization, displaying local nucleotide similarities and dissimilarities
Haematococcus lacustris genome assembly and annotation reveal diploid genetic traits and stress-induced gene expression patterns
No full textThe green alga Haematococcus lacustris (formerly Haematococcus pluvialis) ) is a primary source of astaxanthin, a ketocarotenoid with high antioxidant activity and several industrial applications. Here, the Haematococcus lacustris highly repetitive genome was reconstructed by exploiting next-generation sequencing integrated with Hi-C scaffolding, obtaining a 151 Mb genome assembly in 32 scaffolds at a near-chromosome level with high continuity. Surprisingly, the distribution of the single-nucleotide-polymorphisms identified demonstrates a diploid configuration for the Haematococcus genome, further validated by Sanger sequencing of heterozygous regions. Functional annotation and RNA-seq data enabled the identification of 13,946 nuclear genes, with >5000 genes not previously identified in this species, providing insights into the molecular basis for metabolic rearrangement in stressing conditions such as high light and/or nitrogen starvation, where astaxanthin biosynthesis is triggered. These data constitute a rich genetic resource for biotechnological manipulation of Haematococcus lacustris highlighting potential targets to improve astaxanthin and carotenoid productivity
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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