1,720,961 research outputs found
Phylogenomics
No full textIn der Evolutionsbiologie wurde in den letzten Jahren durch Aufkommen der Phylogenomik ein neues Kapitel aufgeschlagen. Mit Hilfe genomweiter Analysen wird es zunehmend möglich, schwierige Fragestellungen zur Evolutionsgeschichten zu untersuchen, doch diese neuen Perspektiven sind gleichzeitig verbunden mit erhöhter Komplexität und anderen Schwierigkeiten bei der Stammbaumberechnung. Der Fokus dieser Dissertation ist es, Einblicke in Fragen aus der Theorie der Baumrekonstruktion sowie zu Algorithmen und Anwendungen der Phylogenomik zu geben.
Ein Hauptaugenmerk liegt hierbei auf der Untersuchung phylogenetischer Terrassen, dies Speziesbäume mit gleichen Maximum Likelihood oder Maximum Parsimonie Werten. Ein Problem bei der Suche nach optimalen Bäumen ist die Größe der Terrasse. Die Größe der Terrassen hängt dabei entscheidend von dem untersuchten multiple Sequenz Alignment ab.
Im Rahmen dieser Arbeit wird zunächst erklärt wie man Terrassen während der Baumsuche detektiert. Dazu studieren wir durch Partitionen induzierte Bäume und in welcher Weise topologische Umformungen am Speziesbaum Änderungen an den Partitionsbäumen bedingen. Sollte eine Änderung der Verzweigungsstruktur eines Speziesbaum keine Änderung an den mit ihm assoziierten induzierten Partitionsbäumen hervorrufen, gehören sowohl der gegenwärtige als auch der geänderte neue Speziesbaum zur selben Terrasse.
Es werden drei Propositionen bewiesen, die Kriterien definieren nach welchen verschiedene Umformungsoperationen, namentlich NNI (Nearest Neighbour Interchange), SPR (Subtree Pruning and Regrafting) und TBR (Tree Bisection and Reconnection), sich die induzierten Partitionsbäume verändern. Weiters wird das Konzept von Terrassen erweitert, in dem partielle Terrassen definiert werden und ihr Auftreten für echte Alignments unter NNI Umformungsoperationen untersucht wird.
Im zweiten Teil wird die Datenstruktur, PTA, (phylogenetic terrace aware data structure) vorgestellt, die eine effiziente Analyse verknüpfter multipler Alignments unter Berücksichtigung phylogenetischer Terrassen ermöglicht. Mit Hilfe von PTA und den Kriterien zur Erfassung (partieller) Terrassen ist es möglich, überflüssige Neuberechnungen der Maximum Likelihood oder Maximum Parsimonie Werte zu vermeiden und so die für die Baumsuche benötigte Rechenzeit zu verringern. Durch die Identifizierung partieller Terrassen wird im Vergleich zur Standardimplementierung eine bis zu 5-fache Beschleunigung von IQ-TREE festgestellt und nach der Implementierung der Terrassenidentifikation ist IQ-TREE in der Lage bis zu 6 Mal schneller Maximum-Likelihood-Bäume zu finden als RAxML. Die Datenstruktur PTA eignet sich für den Einsatz mit allen Partitionsmodellen und für alle üblichen topologischen Umformungen wie NNI, SPR und TBR.
Im Schlussteil dieser Arbeit werden Methoden für den Einsatz in Naturschutzbiologie und -ökologie eingeführt und diskutiert, wobei Phylogenomik herangezogen wird, um die evolutionäre Diversität verschiedener Spezies zu quantifizieren. Wir diskutieren die Aufgabe der Auswahl überlebensfähiger Taxa, ein Optimierungsproblem unter Einbeziehung von Räuber-Beute-Interaktionen. Zuerst wird dabei der Rahmen der Aufgabenstellung erweitert, um auch die Splitdiversität (SD) zu erfassen, ein Biodiversitätsmaß welches auf der evolutionären Distanz zwischen verschiedenen Spezies in Splitnetzwerken basiert. Danach erweitern wir die Definition von Lebensfähigkeit um die Nahrungszusammensetzung des Räubers miteinzubeziehen und so die Modellierung realistischer zu gestalten. Mit Hilfe der SD und unter Berücksichtigung eines realistischen Modells werden Spezies für Naturschutzmaßnahmen priorisiert. Obwohl derartige Optimierungsaufgaben in den Bereich NP-schwerer Probleme fallen, zeige ich, dass sie mit Hilfe von ILP (Integer Linear Programming) in überschaubarer Zeit gelöst werden können. In dieser Arbeit werden ILP-Ansätze für alle darin diskutierten Problemstellungen beschrieben sowie eine Implementierung im Software Paket PDA bereitgestellt.In the recent years phylogenomics opened a new chapter in evolutionary biology. The analysis of the genome-scale data sets has the potential of answering the most difficult and intriguing questions for evolutionary histories. However, such perspectives come with a higher complexity and difficulties for the phylogenomic inference. The focus of this thesis is exploring and providing insights into some of the questions arisen from theory, algorithms and applications of phylogenomics.
The main contributions of the thesis deal with phylogenetic terraces, which represent sets of species trees in tree space with identical score (likelihood or parsimony).
Firstly, we provide the rules to detect terraces during the tree search. To this end we study the induced partition trees and how topological rearrangements on species tree drive changes on partition trees. If the tree rearrangement operation applied to the current species tree does not change any of its associated induced partition trees, then the current and a new species trees belong to one terrace. We proof three propositions defining the rules when Nearest Neighbour Interchange (NNI), Subtree Pruning and Regrafting (SPR) and Tree Bisection and Reconnection (TBR) operations change the induced partition trees. We further generalize the concept of terraces to partial terraces and study their occurrence for real alignments using NNI neighbourhoods.
Secondly, we provide a phylogenetic terrace aware data structure (PTA) for the efficient analysis of concatenated multiple alignments. Using PTA and the rules developed to detect (partial) terraces in the presence of missing data one saves computational time by avoiding unnecessary recomputations. We implemented PTA in IQ-TREE and tested its performance on 11 real alignments. Identification of partial terraces speeded up the tree search with IQ-TREE for up to 5 and 6 times compared to the standard implementation (terrace-unaware) and RAxML, respectively. PTA is suitable for the use with all partition models and all common topological rearrangement operations, such as NNI, SPR and TBR.
Finally, we develop methods for conservation biology and ecology, where phylogenomics is used to quantify the evolutionary diversity of the species. We discuss the viable taxon selection problem, which incorporates predator-prey interactions to define viability constraints. First, we extend the problem to account for Split Diversity (SD), a biodiversity measure, which is based on the evolutionary distances between species on split networks. Second, to make the viability constraints more realistic we extend the viability definition to account for the diet composition of predators. SD with the viability constraints is used to prioritize species for the conservation actions. Though such optimization problems fall into the area of NP-hard problems, it is possible to solve them within reasonable amount of time using Integer Linear Programming (ILP), a well-known method for the decision-making problems. We provide the ILP formulations for all the discussed problems and implement them in the PDA software package. To exemplify the discussed methods we apply them to a real case study – the Caribbean Coral Reef community
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
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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