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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
Functional characterization of the calcium sensor AtCML8 in the development of Arabidopsis thaliana
No full textLes plantes sont des organismes sessiles extrêmement dépendants de leur environnement. Au cours de l'évolution, elles ont mis en place des voies de signalisation pour assurer une croissance optimale et un développement adapté. Dans ce contexte, la signalisation calcique a été décrite pour contribuer à ces processus. La perception d'un stimulus par les cellules végétales entraine une variation rapide et transitoire de la concentration intracellulaire en calcium ([Ca2+]int) non stéréotypée, appelée "signature calcique". Ce(s) signature(s) peuvent être prise(s) en charge par des senseurs de calcium capables de transduire ce signal à l'échelle cellulaire en interagissant et modulant l'activité de protéines cibles et ainsi déclencher une réponse physiologique adaptée. Au cours de mes travaux, je me suis concentrée sur une classe de senseurs spécifiques aux plantes, extrêmement proches de la calmoduline (CaM), les protéines calmodulin-like ou CMLs. Chez Arabidopsis thaliana, il existe 50 CMLs dont la taille, le profil d'expression et le nombre de domaines de liaison au calcium sont très différents. Les analyses globales de modifications des transcriptomes laissent supposer que les CMLs pourraient être impliquées dans les réponses aux stress de l'environnement ou dans certaines transitions développementales. Les données reportées issues d'analyses fonctionnelles sont peu nombreuses et l'importance de ces CMLs reste globalement méconnue. Mon projet de thèse s'intègre dans ce contexte, mon travail s'est concentré sur la caractérisation d'une des CMLs présente chez Arabidopsis : CML8. J'ai caractérisé fonctionnellement cette calmodulin-like dans un contexte développemental. Par une approche perte/gain de fonction, j'ai montré l'importance de CML8 dans le développement racinaire chez A. thaliana. CML8 agit comme un régulateur négatif de la croissance de la racine primaire. Le gène CML8 est également assez spécifiquement exprimé dans les primordia de racines latérales et les analyses phénotypiques de nos lignées ont montré que CML8 modulerait l'architecture racinaire en participant à la mise en place de racines latérales. Lors de mes travaux, j'ai pu montrer que CML8 était étroitement liée à la voie des brassinostéroïdes (BR). Une analyse RNA-seq a permis de montrer que près de 40% des gènes différentiellement exprimés dans les lignées cml8 étaient connus pour être régulés par les BRs. Parmi ces gènes sont identifiés des acteurs de l'expansion cellulaire ou des régulateurs des crosstalks hormonaux BRs-Auxine qui pourraient expliquer les phénotypes observés. CML8 interviendrait en amont de ces voies car j'ai pu montrer l'interaction in planta de CML8 avec BRI1, le récepteur clé des BRs. La modulation du niveau d'expression de CML8 (KO vs OE) affecte la voie de signalisation des BRs en perturbant l'état de phosphorylation d'un facteur de transcription clé de la voie (BES1) et en altérant l'expression de gènes de l'homéostasie des BRs. L'effet de l'interaction CML8/BRI1 reste à explorer d'un point de vue biochimique mais afin de mieux comprendre les modalités d'interactions CML-partenaires, j'ai engagé 2 approches qui sont (i) l'identification sans a priori du premier répertoire de partenaires d'une CML une approche de co-immunoprécipitation in planta et (ii) étudier la possibilité d'un mode de régulation alternatif (i.e. en plus de la liaison au Ca2+) des senseurs de type CaM et CML via des modifications post-traductionnelles.Plants are sessile organisms that are highly dependent on their environment. During evolution, they have developed signalling pathways to ensure optimal growth and development. In this context, calcium signalling has been described to contribute to these processes. The perception of a stimulus by plant cells results in a rapid and transient change in the intracellular calcium concentration called the 'calcium signature'. This signature(s) can be processed by calcium sensors that are able to transduce this signal at the cellular level by interacting with and modulating the activity of target proteins and thus triggering an appropriate physiological response. During my PhD, I have studied a class of plant-specific sensors that are closely related to calmodulin (CaM), the calmodulin-like proteins or CMLs. In Arabidopsis thaliana, there are 50 CMLs and transcriptome analyses suggest that CMLs may be involved in responses to environmental stresses or in certain developmental transitions. However, functional analyses data remain scarce and the importance of these CMLs is still largely misunderstood. My thesis project is part of this context and my work has focused on the characterization of CML8, a CML of the model plant A. thaliana. I have functionally characterised this CML in a developmental context. Using a loss/gain of function approach, I have demonstrated the importance of CML8 in Arabidopsis root development by showing that CML8 acts as a negative regulator of primary root growth. The CML8 gene is rather specifically expressed in lateral root primordia and the mutant analyses showed that CML8 modulated the root architecture. My work has led to the finding that CML8 was closely connected to the brassinosteroid (BR) pathway. An RNA-seq analysis revealed that nearly 40% of the genes differentially expressed in cml8 lines were reported to be regulated by BRs. Among these genes, actors of cell expansion or regulators of BRs-Auxin hormonal crosstalks were identified, which could explain the phenotypes observed in the mutants. CML8 would act upstream of these pathways as I have shown in planta the interaction of CML8 with BRI1, the receptor for BR and that modulation of the level of CML8 affects the BR signalling pathway. The effect of the CML8-BRI1 interaction still need to be explored from a biochemical point of view but to better understand the CML-partner interactions I have engaged 2 approaches which are (i) the in planta identification without a priori of the first repertory of CML-interacting protein and (ii) to study the possibility of post-translational modifications of CaM and CML in plants
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
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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Contribution and regulation of PRR2, a plant specific transcription factor, in plant immunity
No full textLa capacité des plantes à répondre aux stress de l'environnement, qu'ils soient de nature biotique ou abiotique, tient au fait qu'elles sont capables d'intégrer les signaux perçus grâce à des mécanismes de transduction du signal rapides et efficaces. La perception, le décodage et la mise en place de réponses biologiques adaptées font appel à de nombreux acteurs moléculaires tels que le calcium (Ca2+), second messager majeur de la signalisation Eucaryote. Parmi les "senseurs de calcium", la calmoduline (CaM) est la protéine la plus connue. Il existe des protéines apparentées à la CaM, spécifiques aux plantes, les Calmodulin-like (CMLs). Les CMLs sont très peu étudiées et la caractérisation de leurs rôles ouvre de larges perspectives sur l'identification des réseaux de régulation. L'objectif de ce travail de thèse a concerné un partenaire nucléaire d'une de ces CMLs, AtCML9, le Pseudo-Response Regulator 2 (PRR2), une protéine atypique contenant un domaine de liaison à l'ADN de type GARP et de fonction inconnue. Au cours de ce travail, des analyses moléculaires et biochimiques ont permis de caractériser le rôle de PRR2 dans l'immunité végétale, et en particulier en réponse à Pseudomonas syringae. L'étude de lignées perte ou gain de fonction a permis de mettre en évidence que PRR2 agit comme un régulateur positif des défenses lors de l'infection par la bactérie pathogène hémibiotrophe Pst DC3000 à travers la modulation de l'acide salicylique, de composés de défense tels que la protéine PR1 et la camalexine. Les analyses phénotypiques réalisées en réponse à différentes souches de Pseudomonas ont permis de préciser que PRR2 contribue à la mise en place des défenses à travers la signalisation dépendante de l'acide salicylique et de l'injection des effecteurs bactériens. Dans une deuxième partie, l'interaction entre PRR2 et des facteurs de transcription spécifiques aux plantes, les TCPs (Teosinte Branched 1, Cycloidea and PCF), a été étudié. Ces analyses ont montré une spécificité d'interaction entre PRR2 et TCP19 ou TCP20. Ces interactions stabilisent et relocalisent PRR2 dans des domaines nucléaires spécifiques. Ces données suggèrent une forte régulation post-traductionnelle de la protéine PRR2 qui pourrait s'avérer nécessaire à sa fonction biologique.Plants are able to perceive and respond to diverse biotic or abiotic environmental cues. This ability relies on efficient signalling pathways that are ultimately associated with genetic reprograming. These responses involve various actors of the signalling pathways such as calcium (Ca2+) transients which act as a second messenger in eukaryotic cells. The variations in intracellular Ca2+ concentrations are perceived by calcium sensors. The calmodulin (CaM) is an ubiquitous Ca2+ sensor well studied both in animal and plant cells. Comparatively, plants also possess CaM-related proteins called Calmodulin-like (CMLs) which are less studied and their role in plant physiology are emerging. The objective of this PhD work was to perform the functional analysis of PRR2 (Pseudo-Response Regulator 2), a plant specific transcription factor (with a GARP DNA binding domain) previously identified as an AtCML9-interacting partner. Using diverse genetic tools, we were able to study the role of PRR2 in plant immunity using the model plant Arabidopsis thaliana and a phytopathogenic bacteria, Pseudomonas syringae. Our study has shown that PRR2 acts as a positive regulator of plant defenses upon bacterial infection. We show that PRR2 could act by modulating the biosynthesis of the salicylic acid (SA), and the production of defense-associated compounds such as PR1 and camalexin. Collectively our data indicate that PRR2 acts as a positive regulator of plant defense associated with SA. In the aim to better understand how PRR2 could be involved in different physiological responses, we search for PRR2-interacting partners. We have more precisely worked on the interactions between PRR2 and the TCPs (Teosinte branched 1, Cycloidea and PCF) which are also plant specific transcriptions factors involved in different biological processes. We showed that PRR2 specifically interact with TCP19 or TCP20. As consequences, these interactions stabilize PRR2 and relocalize the complex in specific nuclear subdomains
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