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Pathways to Function via the Emergence of a Mechanical Switch in Evolvable Matter
No full textThe underlying principles of how sharp switches occur in rugged fitness landscapes, while integral for understanding evolution of function and adaptation in biological systems, remain elusive. Here I use elastic mechanical networks as a platform for probing the physical principles governing single-mutation transitions between two highly-fit, incompatible functions. The function used is an allosteric coupling of two pairs of source and target nodes that respond to an input strain in-phase or out-phase with each other. I study the complete fitness landscapes for ensembles of networks, and find that high-fitness pathways between these functions nearly always exist. At the largest fitness threshold for viable evolution, the functional transitions occur via a “jumper” mutation: a single bond addition or deletion that connects distinct fitness peaks with opposite functions. These mutations can be viewed as a mechanical switch, which I find can switch between incompatible functions with minimal perturbation to the system. In some cases, the mere presence of a bond, regardless of stiffness, constrains the deformation mode and determines function. However, bond formation or breaking is not always necessary: subtle geometric deformations that conserve connectivity can be sufficient to induce sharp functional transitions. The study of this physical system suggests that the single mutation function switches often found in biological systems may be fundamentally mechanical in origin
Epistatic pathways in evolvable mechanical networks
Full text linkAn elastic spring network is an example of evolvable matter. It can be pruned to couple separated pairs of nodes so that when a strain is applied to one of them, the other responds either in-phase or out-of-phase. This produces two pruned networks with incompatible functions that are nearly identical but differ from each other by a set of mutations, each of which removes or adds a single bond in the network. The effect of multiple mutations is epistatic; that is, the effect of a mutation depends on what other mutations have already occurred. We generate ensembles of network pairs that differ by a fixed number, , of discrete mutations and evaluate all mutational paths between the in- and out-of phase behaviors up to . With a threshold response for the network to be considered functional, so that non-functional networks are disallowed, only some mutational pathways are viable. We find that there is a surprisingly high critical response threshold above which no evolutionarily viable path exists between the two networks. The few remaining pathways at this critical value dictate much of the behavior along the evolutionary trajectory. In most cases, the mutations break up into two distinct classes. The analysis clarifies how the number of mutations and the position of a mutation along the pathway affect the evolutionary outcome
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
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Evolutionary pathways in epistatic mechanical networks
No full textAn elastic spring network is an example of evolvable matter. It can be pruned to couple separated pairs of nodes so that when a strain is applied to one of them, the other responds either in-phase or out-of-phase. This produces two pruned networks, with incompatible functions, that are nearly identical but differ from each other by a set of “mutations” each of which removes or adds a single bond in the network. We generate ensembles of network pairs that differ by a fixed number, M, of discrete mutations and evaluate all M! mutational paths between the in- and out-of-phase behaviors up to M 14. With a threshold response for the network to be considered sufficiently fit for either function, so that nonfunctional networks are disallowed, only some mutational pathways are viable. We find that there is a surprisingly high critical response threshold above which no evolutionarily viable path exists between the two networks. The few remaining pathways at this critical value dictate much of the behavior along the evolutionary trajectory. The effect of multiple mutations is epistatic, that is, the impact of a mutation is not invariant but depends on what other mutations have already occurred. In most cases, the mutations break up into two distinct classes based on epistasis. The analysis clarifies how the number of mutations and the position of a mutation along the pathway affect the evolutionary outcome
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
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