1,721,071 research outputs found
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
Structural and functional study of proteins involved in normal and aberrant mRNA decay in Saccharomyces cerevisiae
No full textLa traduction des ARNm en protéine est un processus finement régulé grâce aux mécanismes développés par la cellule pour en contrôler l’efficacité et la fidélité. En effet, les ARNm sont sujets à diverses erreurs au cours de leur transcription et leur maturation. En particuliers, les erreurs entrainant l’apparition de codons stop précoces peuvent conduire à la synthèse de protéines tronquées à effet néfaste sur la cellule. C’est pour cela que de tels ARNm sont rapidement dégradés grâce à un mécanisme régulateur appelé la NMD (Nonsence mediated mRNA Decay). Chez la levure Saccharomyces cerevisiae, cette voie est régie par l’action coordonnée des protéines Upf1, Upf2 et Upf3 formant le complexe de surveillance, mais elle fait également intervenir les facteurs de terminaison classique eRF1 et eRF3, ainsi que d’autres facteurs peu caractérisés tels que la protéine Ebs1. Par ailleurs, la dégradation de ces ARNm défectueux est accélérée par la dégradation rapide de la coiffe ou « decapping ». Au cours de ce travail, nous avons caractérisé des domaines fonctionnels de protéines impliquées dans la détection et la dégradation de ces ARNm. En particuliers, nous nous sommes intéressés à l’étude structurale de la protéine Upf2 qui constitue l’élément central du complexe de surveillance. Nous avons également caractérisé un domaine de la protéine Pat1, puissant activateur du « decapping ». Cette étude nous a permis de mieux comprendre le rôle de ces protéines dans le contrôle qualité et la dégradation des ARNm.MRNA translation process is finely tuned thanks to the regulatory mechanisms evolved by the cell controlling its rate, efficiency and fidelity. Indeed, mRNAs are often subjected to transcription and maturation errors. In particular, mRNA harboring premature stop codons (PTC) in their open reading frames could be translated into truncated proteins with a deleterious impact on the cell. Thus, such mRNAs are rarely detected in the cell as they are rapidly degraded thanks to the NMD (Nonsence mediated mRNA Decay) pathway. In yeast Saccharomyces cerevisiae, this process is governed by the Upf1, Upf2 and Upf3 proteins forming the “surveillance complex”, the termination factors (eRF1 and eRF3) as well as some other poorly characterized factors like Ebs1 protein. In addition, degradation of such mRNAs is enhanced by rapid degradation of the 5’ cap or decapping. In this work, we focused on the characterization of some proteins involved in this process. In particular, we addressed the structural characterization of Upf2 protein, the central component of the surveillance complex. In addition, we characterized a functional domain of Pat1 protein, a strong decapping enhancer. This study allowed us to give a new insight into the role of these proteins in mRNA quality control and decay
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
Structural and functional characterization of protein complexes involved in the elimination of aberrant mRNAs
No full textL’ARN messager (ARNm) produit à partir de l’ADN sert de matrice au ribosome pour la production de protéines dans les cellules. Le rôle majeur de l’ARNm dans le transfert de l’information explique la présence de nombreux mécanismes de contrôle qualité le concernant.Parmi ces contrôles qualités se trouve la voie « non-sense mediated mRNA decay » (NMD). Celle-ci permet la dégradation des ARNm porteurs d’un codon stop précoce (PTC). L’élimination de ces ARNm aberrants permet d’éviter l’accumulation de protéines tronquées dans la cellule. Bien que mis en évidence en 1979, le mécanisme de la voie NMD, à ce jour, ne fait pas consensus. De nombreuses études ont été menées chez différents organismes (humain, levure, ver) et certains arguments se contredisent rendant difficile l’établissement d’un modèle unique.La protéine Upf1 est reconnue comme étant l’acteur central de la voie NMD. Cette enzyme a de nombreux partenaires. Son implication au sein de deux complexes distincts et successifs chez la levure a été mise en évidence en 2018. Le premier complexe composé des protéines historiques de la voie NMD : les protéines Upf1, Upf2 et Upf3, serait responsable de la discrimination entre un codon stop précoce et un codon stop normal. Le second organisé autour d’Upf1 permettrait la dégradation de l’ARNm cible. Au sein de ce second complexe dit effecteur, se trouve les protéines du complexe de decapping connues pour altérer l’intégrité de l’ARNm mature ainsi que les protéines Nmd4 et Ebs1. Le rôle précis de ces dernières n’est pas connu mais elles possèdent toutes deux des homologues humains fortement étudiés. Par analyse de séquence, Ebs1 est proche de la protéine humaine hSMG7 qui est responsable du recrutement du complexe de déadénlyation CCR4-NOT. L’homologue humain de Nmd4 serait hSMG6, responsable de coupure endonucléolytique dégradant l’ARN ciblé.Cette thèse se concentre sur l’étude de la protéine de levure Nmd4. L’étude de la protéine seule a permis de valider son repliement prévu en domaine de type PIN. Ce type de repliement est caractéristique des endonucléases. Cependant la non-conservation d’un résidu conservé dans le site catalytique met en doute la conservation de cette activité présente chez l’Homme. Dans un second temps, l’interaction entre Nmd4 et le domaine central de la protéine Upf1 a été validée, le complexe correspondant ayant été reconstitué. La structure de ce complexe a été résolue par cristallographie aux rayons X et a permis de mettre en évidence le rôle majeur de l’extrémité C-terminale de Nmd4 dans cette interaction. Plusieurs techniques ont permis de valider ce rôle majeur, notamment la diminution de cette interaction par mutagenèse dirigée confirmant l’implication d’un motif précis.De manière intéressante la protéine humaine SMG6 (homologue de Nmd4) interagit avec Upf1 de deux manières différentes : selon des interactions phospho-dépendantes mais également selon des interactions phospho-indépendantes. Une analyse bio-informatique couplée par une étude in cellulo a permis de mettre en évidence que le motif d’interaction responsable de l’interaction chez la levure, permet également une interaction phospho-indépendante entre hSMG6 et hUPF1. Cette conservation entre les deux organismes permet de commencer à unifier les modèles proposés.Produced from the DNA in the nucleus, messenger RNAs (mRNAs) are the matrix for the production of proteins in the cell. Due to the central role of mRNAs in the transmission of information, many quality control pathways exist regarding their integrity and the message they are carrying.The NMD pathway is responsible for the degradation of mRNAs bearing premature stop codon (PTC). Their specific degradation is fundamental in the cell to avoid production of truncated proteins and accumulation of ribosomes on aberrant mRNAs. This pathway was discovered in 1979, however, its precise mechanism is still under debate. This pathway has been studied in different organisms: mammals, yeast and worms but the results obtained do not yet converge on a unified model.The main actor of this pathway is the Upf1 protein. In 2018, Dehecq et al. proposed a new model based on their main result. In yeast, Upf1 is part of two distinct complexes. The first one is considered as the detector complex which is composed of the three historical NMD proteins, Upf1, Upf2 and Upf3. The proposed model hypothesizes their involvement in the discrimination between a normal stop codon and a PTC. The second complex Upf1 is involved in, is the so called effector complex. After release of Upf2 and Upf3 many factors are recruited. Among them are the decapping complex (Dcp1, Dcp2 and Edc3), responsible of one major step in mRNA degradation. Two other proteins are present in this second complex: Ebs1 and Nmd4. Their exact function is unknown, but they present some homology with human proteins SMG7 and SMG5, respectively responsible for the recruitment of the deadenylation complex CCR4-NOT and the degradation of mRNA by endonucleolytic cleavage.During my work, I focused on Nmd4 to understand 1) its role in this second complex with Upf1 2) its role in the NMD pathway. First, the Nmd4 structure was determined by X-ray crystallography, confirming its folding as a PIN domain, a common folding for endonucleolytic enzymes. But not all the catalytic residues are conserved so the enzymatic activity of Nmd4 is still undefined. Secondly, I managed to obtain the structure of Nmd4 interacting with the central domain of Upf1, confirming their interaction unravelled in the Dehecq et al. 2018 paper. The resolution by X-ray crystallography of this structure lead to the division of Nmd4 into two domains : the PIN domain, and the hook domain. The latter is the C-terminal domain of Nmd4 and is mainly responsible for the interaction between the two partners. We confirmed this result using different approaches, including destabilization by mutagenesis.Last objective of this thesis work is to unify the NMD pathway model. Nmd4 human ortholog is the enzyme SMG6 (hSMG6). By bioinformatics analysis we hypothesize that the motif responsible for the interaction in Nmd4 hook is also present in hSMG6 and may interact with UPF1. We were able to show that when we apply the same mutations on SMG6 domain than those previously applied on Nmd4, this interaction is destabilized. This result shows presence of a similar interaction between SMG6 and UPF1 in human cells as between Upf1 and Nmd4 in yeast and unifies the NMD pathway model between species
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
Protein L mutants for the crystallization of antibody fragments
No full textIn many cases, antibody and their complexes can be crystallized and their structure determined without major difficulties. The remaining problematic cases may be approached through techniques such as of combinatorial complex crystallization which uses immunoglobulin binding proteins (IBP). The range of lattices that can be made using this method can be expanded by engineering mutants of IBP domains. We have designed Peptostreptococcus magnus protein L (PpL) mutants with altered immunoglobulin light chain binding characteristics. While the wild type PpL has two binding sites, some of the mutants contact the light chain via only one site. Other mutants have combinations of weakened first and second binding sites that modify their crystallization properties and their packing mode. In this study, we have selected PpL mutants with different behavior and that are most useful for crystallization and we present the various packing modes obtained so far
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