1,720,997 research outputs found
Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes
Full text linkCompartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. It is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, however few explicitly model the topology of the membranes themselves. Discrete stochastic simulation of molecular kinetics potentially oers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described by simple mass action chemistry. Moreover, modelling every individual molecular interac- tion in the cell is probably unnecessary and currently impractical. Simulation is a form of computer aided analysis, relying on human inter- pretation to derive meaning. To improve eciency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties. This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version [Sean Sedwards and Tommaso Mazza, Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes, Bioinformatics, 15 October 2007; 23: 2800 - 2802] is available online at: http://bioinformatics.oxfordjournals.org/ [doi:10.1093/bioinformatics/btm416]
Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting
Full text linkMembrane systems were originally introduced as models of computation inspired by the structure and the functioning of living cells. More recently, membrane systems have been shown to be suitable also to model cellular processes. Inspired by brane calculi, a new model of membrane system with peripheral proteins has been recently introduced. Such model has compartments (enclosed by membranes), floating objects, and objects attached to the internal and external surfaces of the membranes. The objects can be processed/transported inside/across the compartments and the transport is regulated by opportune objects attached to the membranes surfaces. We present a stochastic simulator of this model, with a style of syntax based on chemical reactions. We show that the simulator can be particularly useful in modelling biological processes that involve compartments, surface and integral membrane proteins, transport and processing of chemical substances. As examples we present the simulation of circadian clock and the G-protein cycle in yeast
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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