1,722,091 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
Get PDFWe 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
Proteasome-associated endonuclease activity in plants : a key role in degrading viral RNAs?
No full textLe protéasome 20S est un complexe protéique multicatalytique impliqué, de par ses activités protéolytiques, dans le contrôle d’une multitude de processus cellulaires. Outre des activités protéolytiques bien caractérisées, le protéasome 20S présente une activité RNasique, de nature endonucléasique. Chez les végétaux, l’activité RNasique associée au protéasome 20S est capable de dégrader les ARN du Tobacco mosaic virus (TMV, Tobamovirus) et du Lettuce mosaic virus (LMV, Potyvirus). La protéine HcPro du LMV a été démontrée comme interagissant avec le protéasome 20S et inhibant son activité RNasique. Nous avons montré pour la première fois que la sous-unité alpha-5 du protéasome 20S chez Arabidopsis thaliana est porteuse d’une activité RNasique, comme cela a été montré précédemment pour les animaux. Nous avons également identifié un acide aminé important pour l’activité RNasique. Nous nous sommes de plus penchés sur la compréhension du rôle in vivo de l’activité RNasique associée à la sous-unité alpha-5 du protéasome. Pour ce faire, nous avons étudié l’impact de la mutation KO de la sous-unité alpha-5 sur l’infection par des potyvirus. Aucun effet drastique n’a été observé, bien que la mutation KO d’un des deux gènes codant pour alpha-5 entraîne une augmentation de la sensibilité au LMV. Nous avons également généré des plantes transgéniques permettant d’éteindre ou de surexprimer alpha-5. Les résultats préliminaires obtenus sont présentés.The 20S proteasome is a barrel shaped protein complex that plays a central role in many cellular processes because of its three protease activities. It is also associated in vitro with an endonucleasic activity that is very well conserved. In plants, 20S proteasome was found to target in vitro two viral RNA for degradation. Furthermore, it was reported that the Lettuce mosaic virus (LMV, Potyvirus) HcPro protein interferes in vitro with this activity. Since the available data concerning the plant proteasome endonucleasic activity were obtained from organisms belonging to different taxonomic groups, we decided to characterize Arabidopsis thaliana 20S proteasome RNase activity. Here we show for the first time that the A. thaliana proteasome alpha-5 subunit exhibits in vitro a RNase activity as it was previously observed for calf. We also identify an amino acid that is important for RNA degradation. We try to understand the potential alpha-5 RNase activity-associated mechanisms in vivo and the role of HcPro. We thus analyze alpha-5 KO mutants behaviour when faced to potyviral infection. No dramatic effect of the mutation was observed. We also generate transgenic plants that are currently under characterization
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe 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
Testing methods for seed-transmitted viruses : principles and protocols – Sven E. Albrechtsen. 2005. 288 pp. CABI Publishing £55.00 (US$ 110.00) ISBN 0-85-199-016-9
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Analyse du virome et des flux de virus entre populations de carottes cultivées et sauvages
No full textLes technologies de séquençage haut débit (HTS pour High-Throughput Sequencing) appliquées aux études de métagénomiques ont révolutionné notre vision de la biodiversité virale, avec un impact notable dans les domaines du phytodiagnostic et de l'écologie virale, permettant d’identifier tous les virus présents dans un échantillon sans connaissance préalable. Cependant, comme pour toute technologie, les stratégies HTS et les pipelines d’analyses des données générées doivent être validés pour garantir leur fiabilité. Ces évaluations sont basées sur la comparaison des performances théoriques et réelles, en utilisant des communautés virales de composition connue. Néanmoins, de telles études font encore largement défaut dans le domaine de la virologie végétale. Au cours de cette thèse, les défis méthodologiques et les questions écologiques liées à la description et à l'analyse des communautés de virus végétaux ont été abordés. Tout d’abord, des communautés synthétiques de phytovirus de complexités variables ont été utilisées pour évaluer les deux stratégies d'enrichissement des virus les plus utilisées dans les études de métagénomique, à savoir l’analyse des acides nucléiques associés aux virions (VANA, Virion-Associated Nucleic Acids) et l'analyse des ARN double brin (ARNdb). Nos résultats montrent que l'approche de l'ARNdb fournit systématiquement une description plus complète du virome à ARN mais, comme attendu, est peu performante pour les virus à ADN. Par ailleurs, on a pu mettre en évidence une corrélation robuste entre la profondeur de séquençage des échantillons et l'exhaustivité de la description du virome, ainsi que l'influence d'autres paramètres tels que la complexité du virome, l'utilisation de contigs et la longueur minimale des contigs. Dans une approche plus orientée vers des questions d’écologie, le virome de 45 populations de carottes sauvages (Daucus carota ssp. carota) et cultivées (Daucus carota ssp. sativus) récoltées en France et de six populations collectées en Espagne a été analysé en utilisant une approche HTS basée sur l’ARNdb. Les résultats ont permis de constater que: (i) les carottes présentent un virome particulièrement diversifié, riche en nouveaux virus qui ont ensuite été caractérisés au niveau moléculaire et (ii) le virome des carottes cultivées est très différent de celui des carottes sauvages. Les signatures virales entre ces deux populations montrent une présence différentielle de certains virus, mais aussi une prévalence différentielle d'autres virus. Sur la base de l'analyse de plantes individuelles, la diversité génétique des virus transmis par pucerons a été analysée, mettant en évidence une différenciation intraspécifique des populations virales entre hôtes sauvages et cultivés pour plusieurs de ces virus. Il s'agit d'un résultat particulièrement intéressant si l'on considère que les carottes cultivées et sauvages sont membres de la même espèce, et qu'elles représentent donc un pathosystème pour lequel peu de contraintes génétiques et botaniques sont attendues sur le flux de virus entre ces deux populations. Globalement, les résultats obtenus suggèrent un impact majeur des conditions de culture liées à l'agriculture dans la structuration de la richesse et de la composition du virome. Ils ont également montré l'existence de flux viraux entre les compartiments sauvage et cultivé mais aussi l'existence de barrières limitant ou empêchant les échanges de certains virus ou de certains groupes d'isolats viraux. Le pathosystème carotte utilisé ici a permis de mieux comprendre les viromes contrastés qui peuvent s'assembler chez des plantes étroitement apparentées à l'interface agro-écologique et fournissent une base pour des recherches plus approfondies sur les barrières biologiques et écologiques s’appliquant aux mouvements des virus, ainsi que sur les interactions entre virus transmis par pucerons dans un réseau complexe d'interdépendances mutuelles.HTS-based metagenomics has revolutionized our view of biodiversity and has become a powerful tool in plant virus diagnostics and ecology, allowing to theoretically capture without prior knowledge all viruses present in a sample. However, as with any technology, HTS strategies and the corresponding data processing pipelines need to be validated to provide reliable assessments of plant health status and balance the cost of sequencing with the specificity and sensitivity levels required by the study. In this context, metagenomics benchmarking efforts are often based on mock communities of known composition thus allowing to compare the actual vs the expected performance. Despite their importance, such comparative studies in virology are mainly limited to the clinical sector and are largely lacking in the plant virology field. In the present thesis both methodological challenges and ecological questions in relation to the description and analysis of plant virus communities have been addressed. Phytovirus synthetic communities of varying complexity were used to benchmark the two most frequently used virus enrichment strategies for plant virus metagenomics, virion associated nucleic acids (VANA) and double stranded (ds)RNA. The results show that the dsRNA approach systemically provided a more complete description of the RNA virome but, as expected, performed poorly for DNA viruses. A robust correlation between sample sequencing depth and the completeness of virome description was observed, together with the influence of other parameters such as virome complexity, use of de novo assembled contigs and minimal contig length. In a second more ecologically oriented approach the virome of 45 different wild (Daucus carota ssp. carota) and cultivated carrot (Daucus carota ssp. sativus) populations in France and six additional populations in Spain was analyzed using a dsRNA-based HTS approach. The datasets generated have revealed two important findings: (i) carrots exhibit a particularly diverse virome, rich in novel viruses that were then molecularly characterized and (ii) virus communities differ remarkably between wild and cultivated carrots. The contrasting virome fingerprints between field and wild carrot populations involve both differential presence of some viruses and differential prevalence of other viruses. Based on analysis of individual plants by HTS sequencing and RT-PCR, population genetics of aphid-transmitted viruses were analyzed, highlighting intraspecific viral population differentiation between wild and cultivated hosts for several of them. This is a particularly interesting result considering that both cultivated and wild carrots are members of the same species, and thus represent a pathosystem with expected least genetic and botanical constraints on potential virus flow between a crop and its weedy relative. Taken together, the results obtained suggest a major impact of growth conditions created by agriculture in shaping virome richness and composition. They demonstrated the existence of viral fluxes between the wild and cultivated compartments but also the existence of barriers limiting or altogether preventing exchange of some viruses or of some groups of isolates. The carrot pathosystem used here allowed to gain deep insights into the contrasted viromes that can assemble in closely related plants a the agroecological interface and to provide a baseline for further investigations of the biological and ecological barriers to virus movements and on the complex interaction linking aphid-transmitted viruses in a complex network of mutual interdependencies
Sympatric Populations of Crop and Wild Carrots (Daucus carota subsp.) Have Distinct Viromes, with Shared Core Species More Prevalent in Farm-Grown Populations
No full textViral exchanges between crops and wild plants are important considerations in virus ecology and epidemiology but remain poorly understood. To investigate such exchanges, we compared the viromes of wild and farmed carrots (Daucus carota subsp.) growing near each other in France. Farm populations included cultivated varieties and off-type carrots (resembling wild ones) growing among them. This crop–wild relative pathosystem offers notable opportunities for virus exchange due to the hosts’ genetic closeness and geographic proximity. High-throughput sequencing found that viral taxonomic richness was greatest in wild carrots. However, hierarchical clustering and bipartite network analyses revealed that wild and farm carrot viromes differed in their seedborne and vector-borne components. About 50% of viral taxa were shared among population types, whereas others were uniquely associated with either wild or farm carrots. Individual-plant RT-PCR testing of 16 aphid-borne agents from the shared core virome found that their prevalence was generally greatest in farm populations, with some geographic variability in virus pressure. The viromes of off-type and cultivated carrots were most similar, suggesting that proximity and/or management practices influence virome properties. For some aphid-borne viruses, similar isolates were found in wild and cultivated carrots, suggesting exchanges between them or with a shared source. However, isolates of other aphid-borne viruses clustered by carrot type, indicating barriers to viral fluxes that might involve differential susceptibility of populations, vector preferences, or unidentified factors. To improve virus management, we need better understanding of how specific facilitators and barriers of viral exchange can be manipulated to reduce negative viral impacts. [Figure: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license
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