1,720,960 research outputs found
Recombine and survive: evolutionary history of the V highly conserved domain in the mammalian genome after the V-SINE superfamily extinction
No full textShort interspersed elements (SINEs) are non-autonomous retrotransposons. Because of high turnover rate, they exhibit widely divergent nucleotide sequences but highly conserved domains (HCDs) may occur. Three different HCDs originated before the Radiata-Bilateria split and two underwent repeatedly to exaptation. The "V" HCD has been retrieved in 16 nonamniotes'SINE families and within a miniature inverted-repeat transposon, MER6, in the human genome. Through in silico searches in sequenced genomes and transcriptomes, we found MER6 in all primates and its variant, MER6A, in bats and in the star-nosed mole. Moreover, we found evidence of MER6 in a salamander and retrieved its parental Tc1/ mariner element in the painted turtle. Data indicate that MER6 originated by recombination between a V- SINE and the parental Tc1/mariner element. Nucleotide substitution rate, computed on 10 primates orthologous insertions, places MER6 main activity burst as contemporary to Placentalia diversification. Moreover, age analyses suggest that MER6 was no longer active in mammals, except in the tarsier where a recent replication burst originated a new MER6A subfamily. Finally, unlike frog and fishes V-SINEs, genomic distribution of MER6 does not appear biased toward genic regions in human, chimp and mole genomes. Present data show how the V domain managed to survive and replicate after V-SINEs extinction. Although the impact of HCDs is still unclear, their wide conservation suggests some role; the study of V- elements with different replicative biology may help to disentangle transposon- related aspects from putative HCD function
The interplay between genome organization and nuclear architecture of primate evolutionary neo-centromeres
No full textAn Evolutionary Neo-Centromere (ENC) is a centromere that emerged in an ectopic region of a chromosome during evolution. It is thought that the old centromere must be inactivated because dicentric chromosomes are not viable. The aim of the present study was to investigate whether 3D arrangement in the interphase nucleus of the novel and old centromeric domains were affected by the repositioning event. The data we present here strongly indicate that the ENC phenomenon does not affect the 3D location of either novel or old centromeres. Very likely, other features, such as gene density, rather than the newly acquired or lost functions, define positioning in the nucleus
Evolutionary-new centromeres preferentially emerge within gene deserts
Full text linkBACKGROUND: Evolutionary-new centromeres (ENCs) result from the seeding of a centromere at an ectopic location along the chromosome during evolution. The novel centromere rapidly acquires the complex structure typical of eukaryote centromeres. This phenomenon has played an important role in shaping primate karyotypes. A recent study on the evolutionary-new centromere of macaque chromosome 4 (human 6) showed that the evolutionary-new centromere domain was deeply restructured, following the seeding, with respect to the corresponding human region assumed as ancestral. It was also demonstrated that the region was devoid of genes. We hypothesized that these two observations were not merely coincidental and that the absence of genes in the seeding area constituted a crucial condition for the evolutionary-new centromere fixation in the population. RESULTS: To test our hypothesis, we characterized 14 evolutionary-new centromeres selected according to conservative criteria. Using different experimental approaches, we assessed the extent of genomic restructuring. We then determined the gene density in the ancestral domain where each evolutionary-new centromere was seeded. CONCLUSIONS: Our study suggests that restructuring of the seeding regions is an intrinsic property of novel evolutionary centromeres that could be regarded as potentially detrimental to the normal functioning of genes embedded in the region. The absence of genes, which was found to be of high statistical significance, appeared as a unique favorable scenario permissive of evolutionary-new centromere fixation in the population
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
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