1,720,960 research outputs found
Patch Area and Uniform Sampling on the Surface of Any Ellipsoid
No full textSource code (C++), run script (shell), and analysis scripts (Python) in relation to the article "Patch Area and Uniform Sampling on the Surface of Any Ellipsoid
The Role of Aspherical Protein Shape: Dynamic Simulation of Ellipsoids
Full text linkIt was recently discovered that proteins, as well as their constituent amino acids, have aspect ratios that distribute around a value close to the Golden ratio, φ ≈ 1.618. In addition, it has long been known that proteins have an aspherical shape. However, reasons for evolution to favour such a shape have not been investigated. Therefore, in this thesis, possible reasons for proteins to favour a Golden shape are investigated. In order to do this, tri- axial ellipsoids were used as proxies for proteins, with diffusion and packing of ellipsoidal objects. In Chapter 1, the properties of the Golden ratio are discussed, and the relevant literature regarding protein shape, diffusion and packing reviewed. Chapter 2 outlines a Monte Carlo Brownian dynamics algorithm that was developed here to simulate the diffusion and packing of ellipsoidal particles, which interact via the Lennard-Jones potential. This simulation methodology includes two types of boundary: periodic boundary conditions, and a container that is itself ellipsoidal. In Chapter 3, diffusion of ellipsoids is investigated at various fixed volume fractions, using the method- ology of Chapter 2. It was found that the critical volume fraction, at which long-time self diffusion ceases, is greatest for ellipsoids of shape close to that of proteins. This implies that the shape of proteins offers optimal resistance to glass formation. Furthermore, the distribution of random contacts on the ellipsoid surface under diffusion was studied, necessitating the development of a fast means of calculating geodesic distances on the ellipsoid. It was found that the ellipsoidal shape of proteins gives rise to an anisotropic distri- bution of random collisions on their surface, with protein binding sites most common away from points of most probable contact, thus suggesting that an ellipsoidal shape helps to prevent aggregation of proteins. In Chapter 4, the algorithm of Chapter 2 is extended to simulate diffusion driven packing of ellipsoids, one result of which was a greater obtained volume fraction for ellipsoids than for spheres, consistent with previous work regarding ellipsoid packings. It was additionally found that packing of ellipsoids into a spherical container is more efficient than that inside an ellipsoid, with surface order- ing playing a key role in packing efficiency. This surface ordering was not found to occur for amino acids within proteins, due to the lack of a physi- cal boundary inducing torque. Chapter 5 investigates another phenomenon featuring the Golden ratio. Namely, that of quasicrystals, which are ordered arrangements of points in space without periodicity. The question of whether a protein quasicrystal can be made was investigated by identifying proteins that resemble a Golden rhombohedron as potential quasicrystal candidates
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
The Role of Aspherical Protein Shape: Dynamic Simulation of Ellipsoids
Full text linkIt was recently discovered that proteins, as well as their constituent amino acids, have aspect ratios that distribute around a value close to the Golden ratio, φ ≈ 1.618. In addition, it has long been known that proteins have an aspherical shape. However, reasons for evolution to favour such a shape have not been investigated. Therefore, in this thesis, possible reasons for proteins to favour a Golden shape are investigated. In order to do this, tri- axial ellipsoids were used as proxies for proteins, with diffusion and packing of ellipsoidal objects. In Chapter 1, the properties of the Golden ratio are discussed, and the relevant literature regarding protein shape, diffusion and packing reviewed. Chapter 2 outlines a Monte Carlo Brownian dynamics algorithm that was developed here to simulate the diffusion and packing of ellipsoidal particles, which interact via the Lennard-Jones potential. This simulation methodology includes two types of boundary: periodic boundary conditions, and a container that is itself ellipsoidal. In Chapter 3, diffusion of ellipsoids is investigated at various fixed volume fractions, using the method- ology of Chapter 2. It was found that the critical volume fraction, at which long-time self diffusion ceases, is greatest for ellipsoids of shape close to that of proteins. This implies that the shape of proteins offers optimal resistance to glass formation. Furthermore, the distribution of random contacts on the ellipsoid surface under diffusion was studied, necessitating the development of a fast means of calculating geodesic distances on the ellipsoid. It was found that the ellipsoidal shape of proteins gives rise to an anisotropic distri- bution of random collisions on their surface, with protein binding sites most common away from points of most probable contact, thus suggesting that an ellipsoidal shape helps to prevent aggregation of proteins. In Chapter 4, the algorithm of Chapter 2 is extended to simulate diffusion driven packing of ellipsoids, one result of which was a greater obtained volume fraction for ellipsoids than for spheres, consistent with previous work regarding ellipsoid packings. It was additionally found that packing of ellipsoids into a spherical container is more efficient than that inside an ellipsoid, with surface order- ing playing a key role in packing efficiency. This surface ordering was not found to occur for amino acids within proteins, due to the lack of a physi- cal boundary inducing torque. Chapter 5 investigates another phenomenon featuring the Golden ratio. Namely, that of quasicrystals, which are ordered arrangements of points in space without periodicity. The question of whether a protein quasicrystal can be made was investigated by identifying proteins that resemble a Golden rhombohedron as potential quasicrystal candidates
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
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