1,720,981 research outputs found
rNA: a Fast and Accurate Short Reads Numerical Aligner
No full textThe advent of high-throughput sequencers (HTS) introduced the need of new tools in order to analyse the large amount of data that those machines are able to produce. The mandatory first step for a wide range of analyses is the alignment of the sequences against a reference genome. We present a major update to our rNA (randomized Numerical Aligner) tool. The main feature of rNA is the fact that it achieves an accuracy greater than the majority of other tools in a feasible amount of time
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
Transcriptome analysis of brain, intestine and hypopharyngeal glands of Apis mellifera using the Oxford Nanopore third generation sequencing technology
No full textIntroduction
Apis mellifera plays a crucial role in biodiversity and ecological balance. So far, honey bee transcriptome and its modifications induced by stress or pathogens have been poorly studied. Thus, the characterization of the transcriptional profiles of key organs in response to biotic and abiotic factors could fill these gaps and provide new knowledge.
Materials and Methods
Honey bees from four apiaries in Northern Italy were collected and immediately frozen in liquid nitrogen. Brain, hypopharyngeal glands, and intestine were excised and total RNA was extracted from four pools of each tissue (1 pool = 3 bees from a single apiary). Twelve tissue-specific cDNA libraries were constructed and sequenced using the Nanopore Mk1C. State-of-the-art software were used for raw data analysis, reads alignment, and splicing isoforms detection.
Results
About 27 million sequences per tissue were obtained. A total of 55,651 isoforms were identified, of which 21,501 were expressed in at least one of target tissues. Out of these, 6,719 transcripts were annotated, while 10,071 were identified as novel transcripts. The brain showed the highest number of transcripts (14,689), followed by the intestine (8,953) and hypopharyngeal glands (5,227). The analysis of differential expression among the tissues highlighted 2,371 differentially expressed transcripts (DETs), of which 1,236 with known biological function and 715 novel transcripts. The most abundant DETs were those 'activated' exclusively in the brain (some opsins, crucial for vision, and a gene with a fundamental role in longevity) or intestine (genes involved in apoptosis). Several DETs were moderately, but differentially, expressed in all the target organs. As an example, Glutathione S-transferase theta-3 and peroxiredoxin 6 genes, involved in oxidative stress response, were significantly more ‘activated’ in the intestine and hypopharyngeal glands.
Discussion and Conclusion
The present study, carried out within the RC IZS VE 09/20 project and funded by the Ministry of Health, has improved the knowledge of the transcriptome of three key organs of A. mellifera and investigated its complexity by identifying new transcripts. Therefore, it represents a valuable basis for further molecular investigations into honey bee response to environmental stress
G. Progress in the sequencing of tomato chromosome 124th Solanaceae Genome Workshop, Jeju 9/13 Settembre. Pag.164, Abstract Poster – P36 (2007).
No full textDispelling 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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