1,720,993 research outputs found
Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines
Full text linkTechnological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial
community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria
present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these
data.MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights IntoMicrobial Ecology
(QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies. Here, we report
the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic
assignment and in diversity analysis.We found that taxonomic assignment was more accurate with QIIME which, at family level,
assigned a significantly higher number of reads.Thus, QIIME generated a more accurate BIOM file, which in turn improved the
diversity analysis output. Finally, although informatics skills are needed to install QIIME, it offers a wide range of metrics that are
useful for downstream applications and, not less important, it is not dependent on server times
A common microbial signature is present in the lower airways of interstitial lung diseases including sarcoidosis
Full text linkBackground: The etiology of pulmonary sarcoidosis is not well established. Although the mechanism triggering pulmonary sarcoidosis remains to be established, inflammatory reactions seem to play an important role in this process. Objectives: The aim of this study was to define the composition of the lower airway microbiota in the bronchoalveolar lavage (BAL) of patients affected by interstitial lung diseases, including sarcoidosis, to determine whether the bacterial signature differs among these diseases. Methods: Ten patients affected by pulmonary sarcoidosis and 9 patients affected by other interstitial lung diseases were enrolled. 16S rRNA next-generation sequencing was used to study BAL microbial composition of these patients, and were also compared with already published microbial content in higher airways of such diseases. Results: Four phyla dominated the lower airway microbiota, Bacteroidetes being the most abundant phylum in both groups (56.9%). Diversity analysis showed no significant differences between the various diseases, particularly between pulmonary sarcoidosis and other interstitial lung diseases affecting lower airways. Conclusions: Our data indicate that the bacterial lower airways microbiota share the same signature and, therefore, cannot be used as a diagnostic tool to discriminate among different interstitial lung diseases, including sarcoidosis, while microbial diversity is present when considering lower or higher respiratory airways
An Altered Gut Microbiome Profile in a Child Affected by Crohn's Disease Normalized After Nutritional Therapy
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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
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