1,720,989 research outputs found
Pitfalls in bacteria recognition: a 16S rRNA gene sequencing-based simulation study on the oral microbiome environment
Full text linkMicrobiome research has evolved rapidly and became an important topic over the years. The study of the microbiome permits us to investigate bacteria living in specific body sites and to understand its role in host health and disease conditions, observing the structure, function, and interaction between the different compounds. The amplicon sequencing is the most widely used technique to get the diversity composition of the microbiota. In particular, the 16S rRNA gene is the commonly adopted marker gene to identify microbial communities within the human host, collecting information on their relative abundance. In this elaborate we proposed a bioinformatic analysis of the 16S rRNA gene, performing a taxonomical classification of bacteria residing in the human oral cavity, and simulating a microbiome environment, dissecting, and pointing out what are the weak points of an analysis carried out by amplicons sequencing. To detect the microbial composition in 4 oral healthy individuals, the analysis was performed across the 16S rRNA gene amplicon regions by sequencing 6 amplicons involving 2 or 3 consecutive 16S rRNA hypervariable regions. We used the Divisive Amplicon Denoising Algorithm 2 (DADA2) able to infer the bacteria composition of samples by the detection of Amplicon Sequence Variants (ASVs), offering a single nucleotide resolution study. The public extended Human Oral Microbiota Database (eHOMD) was adopted as reference database to assign the taxonomy to the bacteria sequences. A comparison between all the 16S rRNA gene amplicon region was performed to identify which amplicon region better identified microbial communities. The second and most relevant part of the study was based on the results obtained from the 16S rRNA gene amplicon regions analysis used as reference panel. We developed a 16S rRNA gene-based simulator to mimic a marker gene sequencing process, evaluating what might be the pitfalls that could be encountered by carrying out a targeted metagenomic analysis. We selected the full-length 16S rRNA gene sequences from the eHOMD database and we subdivided the sequences into different amplicon regions. Then, a taxonomic classification was carried out to assign a taxonomic rank to the simulated amplicons. Taxonomically unassigned bacterial species underwent to multiple sequence alignment combined with a phylogenetic tree construction against all full-length rRNA gene reference sequences of the eHOMD belonging to the possible Species solutions to investigate the sequence identity between them. Our data reported an improved 16S analysis run with DADA2 using the pooled marker gene amplicon regions in which we identified 204 different bacterial species. Overall, the analysis on the unique ASV counts of the pooled 16S rRNA gene reported that approximately 44% of total ASVs achieved the most detailed species-level classification. However, the amplicon region V2V3 proved to be the portion of the 16S rRNA that recognized the highest number of bacteria at the species taxonomic level (135) through the single amplicon analysis. The simulation process, involving the extraction of amplicon sequences from the full-length 16S rRNA gene sequences of simulated bacterial sequences, showed that not all the amplicons can be extracted, suggesting, several 16S rRNA gene amplicon sequences were not amplified, as often happens in the real world. Furthermore, several bacterial species appear to have a high degree of sequence similarity in a given region of the 16S rRNA gene, making classification incomplete in some cases. The use of the simulator will then be useful to understand the sensitivity of the different regions of the 16S rRNA gene in recognizing the presence of pathogenic bacterial species. Our study can then be adopted to build up an accurate catalog of oral ASVs to essay large sample sets (e.g., hundreds of individuals), aiming at improving the taxonomy classification performances
Qui e altrove. Pino Daniele tra i media e le identità.
No full textAttraverso l'analisi dell'evoluzione dell'immagine mediatica del cantante (televisione, interviste, videoclip), il contributo qui proposto si propone di ripercorrere le dinamiche del rapporto tra Pino Daniele e la città, nella prospettiva di sottolineare come questa immagine sia in parte un riverbero dei conflitti che, dagli anni '70 agli anni '90, hanno caratterizzato il rapporto del Sud Italia con la storia e il contesto nazionale.
L’indagine si sofferma su vari punti di svolta di questo processo. In primo luogo,
la lotta continua, sovente espressa nelle apparizioni del Cantautore, tra la memoria dolorosa di una condizione di subalternità e un forte desiderio di riscatto. In secondo luogo, l'analisi degli omaggi post-mortem (docufiction, mostre, Tourist App) mostrerà come il contesto culturale napoletano abbia agito alla maniera di un sistema normalizzante rispetto a una figura all’inizio considerata eccentrica. Un ampio focus è poi concentrato sulla figura di Massimo Troisi e su come l’amicizia tra il comico e la star della musica abbia rappresentato la “new wave” napoletana degli anni ’90
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
Per un nuovo sound italiano. Arrangiare la canzone attraverso i media negli anni Sessanta
No full textVariations 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
A broad overview of genotype imputation: Standard guidelines, approaches, and future investigations in genomic association studies
Full text linkThe advent of genomic big data and the statistical need for reaching significant results have led genome-wide association studies to be ravenous of a huge number of genetic markers scattered along the whole genome. Since its very beginning, the so-called genotype imputation served this purpose; this statistical and inferential procedure based on a known reference panel opened the theoretical possibility to extend association analyses to a greater number of polymorphic sites which have not been previously assayed by the used technology. In this review, we present a broad overview of the genotype imputation process, showing the most known methods and presenting the main areas of interest, with a closer look to the most up-to-date approaches and a deeper understanding of its usage in the present-day genomic landscape, shedding a light on its future developments and investigation areas
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