1,721,000 research outputs found
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
An improved procedure for clustering and assembly of large transcriptome data
Full text linkMotivations. Expressed sequence tags and full-length cDNAs represent an invaluable source of evidence for inferring reliable gene structures and discovering potential alternative splicing events [1]. However, to fully exploit their biological potential, correct and reliable EST clusters are required. To fill this gap we developed the program EasyCluster that resulted the most accurate when compared to software at the state of the art in this field [2]. Recent technological advances are dramatically increasing the number of available transcriptome reads. EST-like sequences can now be generated by pyrosequencing using Roche 454 platform which generates approximately one million reads per run. Handling such huge amount of EST-like data is basic to detect alternative splicing events, improve gene annotations or simply create gene-oriented clusters for expression studies. Sometimes EST-like data provide a fragmented overview of their genomic loci of origin and, thus, transcript assembly may be an optimal solution to annotate user-produced sequences. For these reasons we propose here a new implementation of EasyCluster able to manage genome scale transcriptome data and generate reliable gene-oriented clusters from 454 reads. The new version of EasyCluster software can facilitate downstream analyses because it enables the assembly of full-length transcripts per cluster, improves the clustering procedure using available annotations and embeds a graphical browser to provide an overview of results at genome level.
Methods. EasyCluster is based on the well-known EST-to-genome mapping program GMAP [3] since it can perform a very quick mapping of whatever expressed sequence onto a genomic sequence and can detect splicing sites according to a so defined "sandwich" dynamic programming that is organism independent. Providing EST-like data from Roche 454 sequencer, EasyCluster initially runs GMAP program and parses results in order to create an initial collection of pseudo-clusters by grouping EST-like reads according to the overlap of their genomic coordinates on the same strand. Then EasyCluster refines the EST grouping by including in each cluster only expressed sequences sharing at least one splice site. An ad hoc procedure is used to correct potential GMAP errors near splice sites and unspliced ESTs are added to each refined cluster. Finally, full-length transcripts are assembled for each cluster in order to valuate the alternative splicing extent and provide gene expression levels according to user supplied annotations.
Results. The new implementation of EasyCluster is written in Java programming language and provides improved clusters of EST sequences. It has been conceived to handle huge amount of EST-like reads produced by Roche 454 machines and supply a unique tool to cluster and assembly such transcriptome reads. Moreover, EasyCluster can now include unspliced reads and take benefit from available annotations. Alternative splicing is also inferred from each cluster after a refining procedure near exon-intron boundaries to reduce mapping errors due to GMAP. Accuracy and performances have been tested on simulated 454 reads by MetaSim software. Preliminary results indicate that the new EasyCluster implementation is highly efficient to manage and analyze deep transcriptome data from Roche 454 technology
Plume activity, magmatism, and the geodynamic evolution of the Central Mediterranean
No full textOn the basis of isotopic and geochemical data we propose that most of the volcanic activity in Italy is plume rather than subduction related. We suggest that a large plume underlies the Tyrrhenian Sea, extending westwards under Sardinia and Corsica, northwards towards the Western Alps and eastwards under the Italian mainland. The plume is isotopically defined in terms of three end-members, different from any of those found in subduction-related environments. Two of the end-members are similar to the FOZO and EM1 mantle components defined on the basis of data from OIBs, while a third, here called ITEM (ITalian Enriched Mantle), is characterized by a high 87Sr/86Sr ratio (> 0.7200) and quite different from any component found in oceanic environments. The two trends that emerge in isotope ratio diagrams indicate mixing between a common end-member (FOZO) and the two others. Implied by the presence of a common end-member is the involvement of a common source and a single large-scale geodynamic system. Partial melting of an isotopically heterogeneous plume head containing both source and entrained material is one way to explain many of the features that characterize Italian magmatism. Widespread extensional tectonics, lithospheric thinning, and deep-seated CO2 emissions add further support to mantle plume activity in Italy
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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