1,720,965 research outputs found
Codon usage indicates that amphibians, reptiles and birds are major hosts for Zika and other arboviruses: implications for epidemiology and surveillance
No full textCodon usage studies estimate the efficiency of viral replication in putative hosts and vectors for which there has been a supposed history of adaptation. This can help reconstructing the global epidemiology of arthropod-borne viruses (arboviruses), clarifying aspects regarding their ecology and evolution. Current studies concentrate on primate hosts, promoting a lack of information about alternative reservoirs. We studied if and how the codon usage of a set of 13 arboviruses comprising Zika, chikungunya, dengue, and yellow fever is adapted to a range of 30 different putative animal hosts. Our results indicate that all considered arboviruses are more adapted to amphibians, reptiles and birds than to humans and other mammals. This outcome is consistent over different indexes and correlates with the same analyses in West Nile and Japanese encephalitis viruses, two arboviruses known for their bird-to-bird transmission cycle. This is an unexpected finding indicating that non-mammals are the likely primary hosts of most arboviruses. Thus, we advocate that wild environments may have a stronger influence than previously thought in the reservoiring and spreading of Zika and other arboviruses. This has profound implications for the actual surveillance and management of outbreaks
On the correct interpretation of similarity index in codon usage studies: Comparison with four other metrics and implications for Zika and West Nile virus
No full textViruses can modify the usage of their synonymous codons to mimic that of their hosts: investigation of codon usage may therefore help increase our understanding of virus biology. The similarity index (SiD or (D(A,B)) is a recent method for estimating the resemblance of the overall codon usage of the hosts to that of a certain virus. Here we report that this index has been systematically misinterpreted in the literature. We first review its mathematical meaning to show that a high value of SiD indicates low codon usage similarity, and not the opposite as frequently reported. We further compared SiD with four other metrics - nCAI, nRCDI, ITE and tAI - using Zika and West Nile arboviruses in relation to various vectors and hosts. We highlight some differences between the five metrics and present a first bioinformatic evidence that Zika virus is poorly adapted to Culex quinquefasciatus, in accordance with the known biology of this virus. We conclude that SiD, if correctly interpreted, is a useful tool for codon studies, but we advocate that the results from this and other methods are context and time dependent and should be taken with car
Using codon usage bias to investigate the role of alternative vectors in the spread of Zika alternative
No full textIn the last years, outbreaks of Zika virus (ZIKV) and Dengue have been reported from both endemic and newly invaded areas areas of the world. ZIKV is in general associated with, and is well adapted to, primates and mosquitoes vectors, on which it can complete its cycle. Unfortunately, there is insufficient information regarding other animal reservoirs and amplification hosts, but there's a concrete possibility that ZIKV can infect other species, including domestic animals both from endemic and newly invaded temperate areas; such knowledge is fundamental to properly describe the epidemiology of ZIKV and plan its management. Unfortunately, large scalescreenings of putative alternative vectors, is extremely time and cost consuming. We suggest to employ Codon Usage Bias (CUB, (the adaptive similarity of codon usage ofvirus to that of its hosts), to predict if alternative hosts, in particular those associated with humans, can vehicle ZIKV. This will be performed by contrasting codon usage of ZIKVof hosts deduced from trascriptomes/proteomes, calculating parameters like RSCU (relative synonymous codon usage), CAI (codon adaptation index) and ENC (effective number of codons). Our first results indicate that Zika has putatively poor replication efficiency in Culex Pipiens. Ultimately, we advocate the analyses of CUB to understand evolutionary dynamics of ZIKV and other flaviviruses and better forecast their future outbreaks
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
Genome-scaled phylogeny of Saccharomyces cerevisiae from spontaneous must fermentations
Full text linkModern winemakers commonly inoculate selected S. cerevisiae strains in must to obtain controlled fermentations and reproducible products. However, wine has been produced for thousands of years using spontaneous fermentations from wild strains, a practice that is experiencing a revival among small wine producers. Despite the widespread usage of such strains in the past, there is much to know about their ecology, evolution and functional potential. For example, the reciprocal affinities of these strains within the S. cerevisiae phylogeny have yet to be discovered, as well as the degree of their biodiversity and their impact on wine terroir. To fill this knowledge gap, we aim at characterising at strain level the S. cerevisiae present in spontaneously fermented musts sampled across Italy. We set up a protocol based on polyphenols-removing prewashes, followed by whole-genome shotgun sequencing at a depth of 5Gb of DNA per sample. We performed both an assembly-free analysis to reconstruct the strain-level phylogeny of S. cerevisiae strains using the species-specific-marker based StrainPhlAn, and the reconstruction of Metagenome-Assembled Genomes of these strains for downstream functional analyses. To plan conservation acts in a scenario of continuous climate change, we aim at isolating and maintaining strains of interest. We will present preliminary results from the analysis of spontaneous musts sampled at different fermenting stages
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