1,720,961 research outputs found
De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
No full textIn the present work, we assembled and characterized a de novo larval transcriptome of the Atlantic bluefin tuna Thunnus thynnus by taking advantage of publicly available databases with the goal of better understanding its larval development. The assembled transcriptome comprised 37,117 protein-coding transcripts, of which 13,633 full-length (>80% coverage), with an Ex90N50 of 3061 bp and 76% of complete and single-copy core vertebrate genes orthologues. Of these transcripts, 34,980 had a hit against the EggNOG database and 14,983 with the KEGG database. Codon usage bias was identified in processes such as translation and muscle development. By comparing our data with a set of representative fish species, 87.1% of tuna transcripts were included in orthogroups with other species and 5.1% in assembly-specific orthogroups, which were enriched in terms related to muscle and bone development, visual system and ion transport. Following this comparative approach, protein families related to myosin, extracellular matrix and immune system resulted significantly expanded in the Atlantic bluefin tuna. Altogether, these results provide a glimpse of how the Atlantic bluefin tuna might have achieved early physical advantages over competing species in the pelagic environment. The information generated lays the foundation for future research on the more detailed exploration of physiological responses at the molecular level in different larval stages and paves the way to evolutionary studies on the Atlantic bluefin tuna
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
Aspects of reproductive biology of the european hake (Merluccius merluccius) in the northern and central adriatic sea (gsa 17-central mediterranean sea)
Full text linkThe study focused on the macroscopic, histological, and biometric analysis of European hake females in GSA 17 (Central-North Adriatic Sea). From 2013 to 2015, 976 females were collected and analyzed monthly. Though females in spawning conditions were found during the whole year, the trend of GSI showed a peak of the reproductive season from April to July in 2014 and 2015. HSI and Kn reached the highest values in September, after the spawning peaks. In 2013, the trend of these indices did not highlight an evident peak, probably due to an adverse event that occurred in the previous winter in the Adriatic shelf. The length at first maturity (L50) was estimated by macroscopic and histological approaches, resulting in 30.81 cm for the macroscopical length and 33.73 cm for the histological length; both values are higher than the current catching legal size. For the first time in this area, batch and relative fecundity were estimated. Relative fecundity was similar to the Mediterranean and the Atlantic stocks, whereas batch fecundity values were lower compared to other fishing grounds. Overall, the analysis of reproductive parameters plays a fundamental role in the sustainable management of this resource in an area as overfished as the Central-North Adriatic Sea
Maturity assignment based on histology-validated macroscopic criteria: Tackling the stock decline of the Mediterranean swordfish (Xiphias gladius)
No full textEffective stock assessment relies on the evaluation of the reproductive potential of a population, but this is often achieved using fast, inexpensive, and inaccurate macroscopic indicators of gonadal maturity. Indeed, this approach suffers from high error rates as a result of misclassification and operator errors. Although histology is considered the gold standard to assign reproductive stages, it represents a time-consuming and expensive method. Therefore, cost-effective approaches are currently needed to assess the species-specific reproductive potential and define the correct size at first maturity (L50). In the present study a histology-calibrated method based on the gonadal index (GI) was developed to assign maturity stages to the overfished Mediterranean swordfish (Xiphias gladius), supported by histological classification of gonadal development, an estimation of L50, and an analysis of the reproductive output of this species. The performance of this new method had an overall agreement of 90% with histological data, and the L50 calculated by the GI-based method compared with histology analysis was not statistically different (p > 0.05). Moreover, in order to apply this method without bias, a thorough validation of the relationship between length and gonad weight was carried out and the suitability of the GI to compare individuals of different size and maturity stages was confirmed. The present findings provide a comprehensive picture of the patterns characterizing Mediterranean swordfish reproduction and a promising method to assign maturity stages based on a macroscopic indicator. This method has the potential to be extensively applied during routine fish sampling activities in the field because of its simple requirements
A comparison of reproductive performances in young and old females: A case study on the atlantic bluefin tuna in the mediterranean sea
Full text linkIn the Mediterranean Sea, a demographic substructure of the Atlantic bluefin tuna Thunnus thynnus has emerged over the last decade, with old and young individuals exhibiting different horizontal movements and spatial–temporal patterns of gonad maturation. In the present study, histology and molecular reproductive markers were integrated with the gonad-specific mir-202 gene expression and ovarian localization to provide a comprehensive picture of the reproductive performances in young and old females and investigate the role played by the mir-202 during gonadal maturation. During the reproductive period, old females (>100 kg; 194.6 ± 33.9 cm straight fork length; 11.3 ± 2.7 years old) were found to have greater reproductive performances than younger females (<80 kg; 139.3 ± 18.8 cm straight fork length; 8.4 ± 1.1 years old) according to gene expression results, suggesting a prolonged spawning season, earlier arrival on spawning grounds and/or better condition in older females. The mir-202-5p showed no global changes; it was abundantly expressed in granulosa cells and faintly present in the ooplasm. On the other hand, the mir-202-3p expression profile reflected levels of oocyte maturation molecular markers (star, lhr) and both histological and molecular (casp3) levels of follicular atresia. Overall, old females exhibited greater reproductive performances than younger females, likely reflecting different reproductive dynamics linked to the physical condition, habitat usage and migratory behaviour. These results highlight the importance of preserving large and old females in the context of fishery management. Finally, the mir-202 appears to be a good candidate to regulate the reproductive output of this species in an autocrine/paracrine manner through either stage-or age-dependent processes
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