1,721,030 research outputs found
Molecular simulations of gram-negative bacterial membranes: a vignette of some recent successes
No full textIn the following review we use recent examples from the literature to discuss progress in the area of atomistic and coarse-grained molecular dynamics simulations of selected bacterial membranes and proteins, with a particular focus on Gram-negative bacteria. As structural biology continues to provide increasingly high-resolution data on the proteins that reside within these membranes, simulations have an important role to play in linking these data with the dynamical behavior and function of these proteins. In particular, in the last few years there has been significant progress in addressing the issue of biochemical complexity of bacterial membranes such that the heterogeneity of the lipid and protein components of these membranes are now being incorporated into molecular-level models. Thus, in future we can look forward to complementary data from structural biology and molecular simulations combining to provide key details of structure-dynamics-function relationships in bacterial membranes
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
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
Towards an interactive tool for the protein docking
No full textMême si le docking protéine-protéine devient un outil incontournable pour répondre aux problématiques biologiques actuelles, il reste cependant deux difficultés inhérentes aux methodes actuelles: 1) la majorité de ces méthodes ne considère pas les possibles déformations internes des protéines durant leur association. 2) Il n'est pas toujours simple de traduire les informations issues de la littérature ou d'expérimentations en contraintes intégrables aux programmes de docking. Nous avons donc tenté de développer une approche permettant d'améliorer les programmes de docking existants. Pour cela nous nous sommes inspirés des méthodologies mises en place sur des cas concrets traités durant cette thèse. D'abord, à travers la création du complexe ERBIN PDZ/Smad3 MH2, nous avons pu tester l'utilité de la Dynamique Moléculaire en Solvant Explicite (DMSE) pour mettre en évidence des résidus importants pour l'interaction. Puis, nous avons étendu cette recherche en utilisant divers serveurs de docking puis la DMSE pour cibler un résultat consensus. Enfin, nous avons essayé le raffinage par DMSE sur une cible du challenge CAPRI et comparé les résultats avec des simulations courtes de Monte-Carlo. La dernière partie de cette thèse portait sur le développement d'un nouvel outil de visualisation de la surface moléculaire. Ce programme, nommé MetaMol, permet de visualiser un nouveau type de surface moléculaire: la Skin Surface Moléculaire. La distribution des calculs à la fois sur le processeur de l'ordinateur (CPU) et sur ceux de la carte graphique (GPU) entraine une diminution des temps de calcul autorisant la visualisation, en temps réel, des déformations de la surface moléculaire.Protein-protein docking has become an extremely important challenge in biology, however, there remain two inherent difficulties: 1) most docking methods do not consider possible internal deformations of the proteins during their association; 2) it is not always easy to translate information from the literature or from experiments into constraints suitable for use in protein docking algorithms. Following these conclusions, we have developed an approach to improve existing docking programs. Firstly, through modelling the ERBIN PDZ / Smad3 MH2 complex, we have tested the utility of Molecular Dynamics with Explicit Solvent (MDSE) for elucidating the key residues in an interaction. We then extended this research by using several docking servers and the DMSE simulations to obtain a consensus result. Finally, we have explored the use of DMSE refinement on one of the targets from the CAPRI experiment and we have compared those results with those from short Monte-Carlo simulations. Another aspect of this thesis concerns the development of a novel molecular surface visualisation tool. This program, named MetaMol, allows the visualisation of a new type of molecular surface: the Molecular Skin Surface. Distributing the surface calculation between a computer's central processing unit (CPU) and its graphics card (GPU) allows deformations of the molecular surface to be calculated and visualised in real time
Vers une nouvelle stratégie pour l'assemblage interactif de macromolécules
No full textProtein-protein docking has become an extremely important challenge in biology, however, there remain two inherent difficulties: 1) most docking methods do not consider possible internal deformations of the proteins during their association; 2) it is not always easy to translate information from the literature or from experiments into constraints suitable for use in protein docking algorithms. Following these conclusions, we have developed an approach to improve existing docking programs. Firstly, through modelling the ERBIN PDZ / Smad3 MH2 complex, we have tested the utility of Molecular Dynamics with Explicit Solvent (MDSE) for elucidating the key residues in an interaction. We then extended this research by using several docking servers and the DMSE simulations to obtain a consensus result. Finally, we have explored the use of DMSE refinement on one of the targets from the CAPRI experiment and we have compared those results with those from short Monte-Carlo simulations. Another aspect of this thesis concerns the development of a novel molecular surface visualisation tool. This program, named MetaMol, allows the visualisation of a new type of molecular surface: the Molecular Skin Surface. Distributing the surface calculation between a computer's central processing unit (CPU) and its graphics card (GPU) allows deformations of the molecular surface to be calculated and visualised in real time.Même si le docking protéine-protéine devient un outil incontournable pour répondre aux problématiques biologiques actuelles, il reste cependant deux difficultés inhérentes aux méthodes actuelles: 1) la majorité de ces méthodes ne considère pas les possibles déformations internes des protéines durant leur association. 2) Il n'est pas toujours simple de traduire les informations issues de la littérature ou d'expérimentations en contraintes intégrables aux programmes de docking. Nous avons donc tenté de développer une approche permettant d'améliorer les programmes de docking existants. Pour cela nous nous sommes inspirés des méthodologies mises en place sur des cas concrets traités durant cette thèse. D'abord, à travers la création du complexe ERBIN PDZ/Smad3 MH2, nous avons pu tester l'utilité de la Dynamique Moléculaire en Solvant Explicite (DMSE) pour mettre en évidence des résidus importants pour l'interaction. Puis, nous avons étendu cette recherche en utilisant divers serveurs de docking puis la DMSE pour cibler un résultat consensus. Enfin, nous avons essayé le raffinage par DMSE sur une cible du challenge CAPRI et comparé les résultats avec des simulations courtes de Monte-Carlo. La dernière partie de cette thèse portait sur le développement d'un nouvel outil de visualisation de la surface moléculaire. Ce programme, nommé MetaMol, permet de visualiser un nouveau type de surface moléculaire: la Skin Surface Moléculaire. La distribution des calculs à la fois sur le processeur de l'ordinateur (CPU) et sur ceux de la carte graphique (GPU) entraine une diminution des temps de calcul autorisant la visualisation, en temps réel, des déformations de la surface moléculaire
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