1,720,992 research outputs found
Role of Magnesium Ions and Ligand Stacking in the Adenine Riboswitch Folding
No full textRiboswitches are RNA structured elements that modulate fundamental pathways in bacteria and plants. Depending on the availability of their sensed metabolite they undergo a conformational change that turns on or off gene expression. In the add adenine riboswitch from Vibrio Vulnificus there are three crucial spots for the switch between the two conformations: the P1 stem, the kissing-loops and the binding site for adenine. Our work is based on advanced in silico techniques, including atomistic molecular simulations, steered molecular dynamics, umbrella sampling, metadynamics and Hamiltonian replica exchange. First we investigated the P1-ligand dependent stabilization quantifying this effect in terms of free energy (Di Palma et al doi:10.1261/rna.040493.113). Then we evaluated the different contributions that Mg2+ and adenine give to the formation of the tertiary interactions between the two loops and we analysed the influence of these interactions on the binding site. The obtained data are in quantitative agreement with experiments. The atomistic description of metabolite binding, RNA-Mg2+ interaction, and tertiary-contact formation clarifies the details of the ligand-aptamer interactions and of the role of divalent cations in the global aptamer folding
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
Atomic-Level Characterization of the Chain-Flipping Mechanism in Fatty-Acids Biosynthesis
No full textDuring fatty acids
biosynthesis the elongating acyl chain is sequestered
within the core of the highly conserved acyl carrier protein (ACP).
At each catalytic step, the acyl intermediates are transiently delivered
from ACP to the active site of the enzymatic counterparts and, at
the same time, are protected from the solvent to prevent nonselective
reactivity. Yet, the molecular determinants of such a universal transitiontermed
chain flippingremain poorly understood. Here we capture the
atomic-level details of the chain-flipping mechanism by using metadynamics
simulations. We observe the fatty-acid chain gliding through the protein–protein
interface with barely 30% of its surface exposed to water molecules.
The small ACP’s helix III acts as gatekeeper of the process,
and we find its conformational plasticity critical for a successful
substrate transfer. The results are in agreement with a wide range
of experimental observations and provide unprecedented insight on
the molecular determinants and driving forces of the chain-flipping
process
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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