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Data accompanying the manuscript "Mechanical interactions in bacterial colonies and the surfing probability of beneficial mutations"
No full textWaclaw, Bartlomiej; Gralka, Matti; Hallatschek, Oskar; Farrell, Fred. (2017). Data accompanying the manuscript "Mechanical interactions in bacterial colonies and the surfing probability of beneficial mutations", 2015-2016 [dataset]. University of Edinburgh. School of Physics and Astronomy. ICMCS. http://dx.doi.org/10.7488/ds/1702
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Evolutionary dynamics in microbial colonies
Get PDFTraditionally, evolutionary biology has mostly taken a retrospective view, looking backwards in time to infer past evolutionary dynamics. Over the past 30 years, evolution experiments in the laboratory have become a valuable complementary technique to study evolution in real time. Microbial populations in shaken flasks are an ideal model system to do this, because their short generation times and easy reproducibility allow for the study of dozens to hundreds of replicates. Our understanding of microbial evolution in these simple laboratory environments has dramatically improved in recent years.Microbial populations in the wild face vastly more complex conditions: they grow as spatially structured communities called microbial biofilms, often consisting of interacting mixtures of different species fulfilling different purposes, subject to various, potentially self-generated, biophysicochemical gradients of, e.g., oxygen or nutrients, which are in turn altered by the physical structure of the community. In short, natural population are subject to a vast variety of ecological interactions, and it has remained unclear how much can be learned from well-mixed liquid culture experiments about how ecology affects evolution in more complex scenarios. In this dissertation, I approach this question using one of the simplest possible ecological aspects: the fact that most populations grow in spatially structured communities. Using microbial colonies as an experimental model system, I examine the effect of spatial structure on evolutionary dynamics in a variety of ways. First, Chapters 2-4 investigate the fates of neutral mutations and the dynamics of beneficial mutations in microbial colonies to find that both the neutral diversity resulting from spontaneous mutations and the strength of adaptation is increased in colonies compared to microbial populations grown in shaken flasks. The second half of the thesis is concerned with the effects of environmental heterogeneity on evolutionary dynamics. In Chapter 5, randomly disordered environments are used to examine the competition of selection and extrinsic noise in a model system for spontaneous beneficial and deleterious mutations. In these experiments, extrinsic noise can almost entirely overpower selection such that beneficial variants cannot leverage their advantage to further their evolutionary success. Chapter 6 discusses the effects of gradients on the emergence of antibiotic resistance and how convective flow can shape the trade-off between selection for resistance and the efficacy of treatment. Overall, the results presented in this thesis suggest that spatial structure can have a momentous influence on the evolutionary dynamics of many dense cellular populations like biofilms and tumors: not only do the dynamics of adaptation change quantitatively in spatially structured populations, but qualitatively different patterns of evolutionary dynamics emerge that cannot arise in well-mixed population. Environmental heterogeneity can also have a strong influence on the speed and the direction of adaptation: whereas random heterogeneity in the environment prevents the spread of beneficial variants, the presence of antibiotic gradients can facilitate the rapid emergence of resistance. This work thus offers a glimpse into the profound and complex ways in which ecology can impact evolution even in simple model systems
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
Get PDFWe 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
Get PDFWe 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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