Dissertations / Theses on the topic 'Evolution Analysis'

It has been argued that much of evolution takes place in the absence of fitness gradients. Such periods of evolution can be analysed by examining the mutational network formed by sequences of equal fitness, that is, the neutral network. It has been demonstrated that, in large populations under a high mutation rate, the population distribution over the neutral network and average mutational robustness are given by the principal eigenvector and eigen- value, respectively, of the network's adjacency matrix. However, little progress has been made towards understanding the manner in which the topology of the neutral network influences the resulting population distribution and robustness. In this work, we build on recent results from spectral graph theory and utilize numerical methods to enhance our understanding of how populations distribute themselves over neutral networks. We demonstrate that, in the presence of certain topological features, the population will undergo an exploration catastrophe and become confined to a small portion of the network. We further derive approximations, in terms of mutational biases, for the population distribution and average robustness in networks with a homogeneous structure. The applicability of these results is explored, first, by a detailed review of the literature in both evolutionary computing and biology concerning the structure of neutral networks. This is extended by studying the actual and predicted population distribution over the neutral networks of H1N1 and H3N2 influenza haemagglutinin during seasons between 2005 and 2016. It is shown that, in some instances, these populations experience an exploration catastrophe. These results provide insight into the behaviour of populations on neutral networks, demonstrating that neutrality does not necessarily lead to an exploration of genotype/phenotype space or an associated increase in population diversity. Moreover, they provide a plausible explanation for conflicting results concerning the relationship between robustness and evolvability.

In this thesis, we study evolution of software architecture and investigate ways to support this evolution.     The central theme of the thesis is how to analyze software evolvability, i.e., a system’s ability to easily accommodate changes. We focus on two main aspects: (i) what software characteristics are necessary for an evolvable software system; and (ii) how to assess evolvability of long-lived proprietary systems in a systematic manner. A secondary focus is to investigate how evolvability is addressed in open source software evolution. We have performed a systematic review of architecture evolution research, and proposed a software evolvability model, in which subcharacteristics of software evolvability and corresponding measuring attributes are identified. Based on this model, we have proposed the softwarearchitectureevolvabilityanalysis (AREA) process which provides repeatable techniques for supporting software architecture evolution: a)                  Qualitative evolvability analysis method that focuses on improving the capability of being able to understand and analyze systematically the impact of change stimuli on software architecture evolution; b)                  Quantitative evolvability analysis method that provides quantifications of stakeholders’ evolvability concerns and potential architectural solutions’ impacts on evolvability. These techniques have been validated in industrial settings of different domains, and can be used as an integral part of software development and evolution process. This is to ensure that the implications of the potential improvement strategies and evolution path of software architectures are analyzed with respect to the evolvability subcharacteristics. As a supplementary research contribution, we have conducted a systematic review of the existing studies in open source software (OSS) evolution, and performed a comprehensive analysis which describes how software evolvability is addressed during the development and evolution of OSS, and identified challenges and future research directions in OSS evolution.

Cette thèse contient des preuves de convergence ou de divergence d'algorithmes d'optimisation appelés stratégies d'évolution (ESs), ainsi que le développement d'outils mathématiques permettant ces preuves.Les ESs sont des algorithmes d'optimisation stochastiques dits ``boîte noire'', i.e. où les informations sur la fonction optimisée se réduisent aux valeurs qu'elle associe à des points. En particulier, le gradient de la fonction est inconnu. Des preuves de convergence ou de divergence de ces algorithmes peuvent être obtenues via l'analyse de chaînes de Markov sous-jacentes à ces algorithmes. Les preuves de convergence et de divergence obtenues dans cette thèse permettent d'établir le comportement asymptotique des ESs dans le cadre de l'optimisation d'une fonction linéaire avec ou sans contrainte, qui est un cas clé pour des preuves de convergence d'ESs sur de larges classes de fonctions.Cette thèse présente tout d'abord une introduction aux chaînes de Markov puis un état de l'art sur les ESs et leur contexte parmi les algorithmes d'optimisation continue boîte noire, ainsi que les liens établis entre ESs et chaînes de Markov. Les contributions de cette thèse sont ensuite présentées:o Premièrement des outils mathématiques généraux applicables dans d'autres problèmes sont développés. L'utilisation de ces outils permet d'établir aisément certaines propriétés (à savoir l'irreducibilité, l'apériodicité et le fait que les compacts sont des small sets pour la chaîne de Markov) sur les chaînes de Markov étudiées. Sans ces outils, établir ces propriétés était un processus ad hoc et technique, pouvant se montrer très difficile.o Ensuite différents ESs sont analysés dans différents problèmes. Un (1,\lambda)-ES utilisant cumulative step-size adaptation est étudié dans le cadre de l'optimisation d'une fonction linéaire. Il est démontré que pour \lambda > 2 l'algorithme diverge log-linéairement, optimisant la fonction avec succès. La vitesse de divergence de l'algorithme est donnée explicitement, ce qui peut être utilisé pour calculer une valeur optimale pour \lambda dans le cadre de la fonction linéaire. De plus, la variance du step-size de l'algorithme est calculée, ce qui permet de déduire une condition sur l'adaptation du paramètre de cumulation avec la dimension du problème afin d'obtenir une stabilité de l'algorithme. Ensuite, un (1,\lambda)-ES avec un step-size constant et un (1,\lambda)-ES avec cumulative step-size adaptation sont étudiés dans le cadre de l'optimisation d'une fonction linéaire avec une contrainte linéaire. Avec un step-size constant, l'algorithme résout le problème en divergeant lentement. Sous quelques conditions simples, ce résultat tient aussi lorsque l'algorithme utilise des distributions non Gaussiennes pour générer de nouvelles solutions. En adaptant le step-size avec cumulative step-size adaptation, le succès de l'algorithme dépend de l'angle entre les gradients de la contrainte et de la fonction optimisée. Si celui ci est trop faible, l'algorithme convergence prématurément. Autrement, celui ci diverge log-linéairement.Enfin, les résultats sont résumés, discutés, et des perspectives sur des travaux futurs sont présentées
In this dissertation an analysis of Evolution Strategies (ESs) using the theory of Markov chains is conducted. Proofs of divergence or convergence of these algorithms are obtained, and tools to achieve such proofs are developed.ESs are so called "black-box" stochastic optimization algorithms, i.e. information on the function to be optimized are limited to the values it associates to points. In particular, gradients are unavailable. Proofs of convergence or divergence of these algorithms can be obtained through the analysis of Markov chains underlying these algorithms. The proofs of log-linear convergence and of divergence obtained in this thesis in the context of a linear function with or without constraint are essential components for the proofs of convergence of ESs on wide classes of functions.This dissertation first gives an introduction to Markov chain theory, then a state of the art on ESs and on black-box continuous optimization, and present already established links between ESs and Markov chains.The contributions of this thesis are then presented:o General mathematical tools that can be applied to a wider range of problems are developed. These tools allow to easily prove specific Markov chain properties (irreducibility, aperiodicity and the fact that compact sets are small sets for the Markov chain) on the Markov chains studied. Obtaining these properties without these tools is a ad hoc, tedious and technical process, that can be of very high difficulty.o Then different ESs are analyzed on different problems. We study a (1,\lambda)-ES using cumulative step-size adaptation on a linear function and prove the log-linear divergence of the step-size; we also study the variation of the logarithm of the step-size, from which we establish a necessary condition for the stability of the algorithm with respect to the dimension of the search space. Then we study an ES with constant step-size and with cumulative step-size adaptation on a linear function with a linear constraint, using resampling to handle unfeasible solutions. We prove that with constant step-size the algorithm diverges, while with cumulative step-size adaptation, depending on parameters of the problem and of the ES, the algorithm converges or diverges log-linearly. We then investigate the dependence of the convergence or divergence rate of the algorithm with parameters of the problem and of the ES. Finally we study an ES with a sampling distribution that can be non-Gaussian and with constant step-size on a linear function with a linear constraint. We give sufficient conditions on the sampling distribution for the algorithm to diverge. We also show that different covariance matrices for the sampling distribution correspond to a change of norm of the search space, and that this implies that adapting the covariance matrix of the sampling distribution may allow an ES with cumulative step-size adaptation to successfully diverge on a linear function with any linear constraint.Finally, these results are summed-up, discussed, and perspectives for future work are explored

In recent years, microRNAs (miRNAs) have been recognised as important genetic regulators of gene expression in Animals and Plants. They can potentially target a large fraction of the cellular transcriptome, having been shown to be important for diverse biological processes such as development, cell differentiation, proliferation and metabolism. The publication of the Human genome in 2001 marked the start of a great community effort to sequence a variety of other species. These data have great potential for comparative genomics, that can lead to better biological understanding. Some miRNA families are known to be highly conserved, across long evolutionary distances, many found in co-transcribed clusters across the genome. While these phenomena have been previously reported, a large-scale analysis of evolutionary patterns was still lacking. Furthermore, the rate at which new relevant data is being made available makes it challenging to keep up and many of the evolutionary studies performed before are now significantly out of date. This thesis describes a number of approaches taken to analyse miRNA datasets, harnessing the full potential of currently available data for comparative genomics. These were used, not only to revisit many of the notions in the field with a larger and updated dataset, but also to develop novel strategies that enable a coherent view of miRNA evolution at different evolutionary time-scales. A new tool, described within this thesis, was developed for large-scale, species independent miRNA mapping. An assessment of the evolution of the miRNA reper- toire across species was performed, together with detailed sequence conservation analysis and miRNA family clustering. Phylogenetic profile analysis uncovered in- teresting co-evolution between miRNAs and protein coding genes. The genomic organisation of miRNAs and their conservation across species was also studied, pro- viding detailed conserved synteny maps for miRNAs and proteins across more than 80 species. Finally, at the intra-specific level, I analysed the occurrence of single nucleotide polymorphisms affecting miRNA loci or their predicted target sites. All the tools built and integrated in this research were made available to the community and designed to be easily updated, making it easier to keep up with the data that is constantly being made available. Many aspects of miRNA biology are still being uncovered, and the ability to easily put these findings into an evolutionary context will potentially be useful for the community.

In the past few years we have witnessed an explosion in the viral genomic data available. GenBank alone holds over 80,000 close to complete viral genomes, and numbers are rising fast. For example, since the submission of the first SARS genome in May 2003, over 140 more have been published. With this genomic data at hand we hope to finally be able to improve our understanding of viruses. Several papers have been dedicated to the study of genome annotation and selection on viral genomes, in particular focusing attention on the evolutionary behaviour of overlapping reading frames. This is a feature common to viruses, where due to the three periodicity of the genetic code, up to three genes may be encoded simultaneously in one direction. The constraints placed on a nucleotide involved in such a multiple coding region will naturally have an effect on its mutational behaviour, and as a result the pattern of evolution will be more complex. Additionally, due to their fast evolution time, we observe changes in gene structure between viruses of the same family. Finally, as a result of this high divergence, alignments between two genomes will tend to be unreliable, thus complicating the issue of comparative analysis further. Our goal is to present methods which may deal with the above mentioned complications. We first introduce an ab initio pairwise comparative annotation method, which not only accounts for the presence of overlapping reading frames in genomes, but also for differences in gene structure between the two compared sequences. Secondly, we develop a hidden Markov model for the annotation of selection strengths across a viral genome accommodating for inter- as well as intragenic differences in selection. Thirdly, we investigate the effect of using a fixed alignment on the inference of selection by incorporating statistical alignment into our selection analysis. All three methods presented here improve on their respective equivalents in the field. We investigate the nature of selection in overlapping regions in several studies, in particular on the genomes of Hepatitis B and HIV2. We provide a full annotation of selection strengths on a nucleotide level for both viral sequences, highlighting fast evolving regions such as the gp120 protein. We also analyse the mutational behaviour of overlapping regions in both genomes and find that in Hepatitis B selection seems to be of equal strength for single and double coding regions. In HIV2, however, single coding regions appear to be under twice as stringent selection as double coding regions, with a tendency for a fast evolving region to overlap a slow evolving one. Each chapter of our work relates to one of our publications. We introduce in turn each method, its academic context and its results. We subsequently in chapter 5 discuss for each method its achievements, its shortcomings and future possible extensions and improvements to it.

In Part A of this project, I insert an RNA affinity tag into the 16S rRNA of O-ribosomes and demonstrate this does not affect their activity. I optimise the purification of O-ribosomes from the mixture of ribosomes in cells, using the affinity tag. I demonstrate that the strategy can be used to purify evolved O-ribosomes and the utility of the purification method by developing an in vitro RF1 termination assay on O-ribosomes. Using this assay I characterise, in vitro, a O-ribosome previously evolved for enhanced unnatural amino acid incorporation in response to an amber codon (Ribo-X). I demonstrate that Ribo-X has a decreased RF1 mediated termination with respect to the progenitor O-ribosome – providing a mechanistic explanation for our in vivo observations. The aim of Part B of this project was to further engineer the orthogonal mRNA-30S complex to prevent cross-reaction with wild type 50S and then to develop a mutant 50S subunit to specifically interact and function with the orthogonal mRNA-30S complex. This would create a fully orthogonal ribosome. A fully orthogonal ribosome would be fully decoupled from translating the proteome. This would set the stage for evolving the large subunit of the ribosome, in particular the PTC to expand the chemical scope of translation. Approaches based on analysis of sequence variation across species and the use random libraries selected O-30S mutants with reduced translational activity with the endogenous 50S. It proved impossible to functionally complement these O-30S mutants with mutant 50S. However, these experiments produced some interesting mutant ribosomes which highlighted possible future approaches to producing a fully orthogonal ribosome.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.
Includes bibliographical references (leaves 112-113).
by Laura M. Durham.
S.M.

In section A, five papers are presented which examine the evolution of HIV-1 both within and between patients. The first paper presented examines the molecular epidemiology of HIV-1 within Scotland, Northern England, and Ireland (paper I), with attention focused on identifying risk group associated differences within the cohort. This work also provides important background information for the interpretation of molecular data from transmission clusters. The main focus of the work on HIV-1 evolution has been on the transmission of HIV-1, with particular emphasis placed on mother-child transmission. Four papers are presented which examine evolutionary aspects of HIV-1 transmission. The first of these (paper II) examines the viral variants transmitted from mother to child in four mother-child transmission pairs. The second (paper III) analyses similar data from five mother-child transmission pairs, focusing predominantly on viral evolution within the child over the first year of life. The final two papers investigating HIV-1 transmission examine viral variation within two transmission sets. Paper IV examines the vertical transmission of HIV-1 to two infected children born to the same mother at an approximately two year interval, while paper V examines the heterosexual transmission of HIV-1 from a male index to two female contacts and the subsequent vertical transmission of HIV-1 to their two children. The phylogenetic placement of these transmission sets within the Edinburgh cohort is also assessed. In section B, four papers are presented which examine aspects of foraminiferal evolution. The first paper (paper I) focuses on the problems inherent in the amplification of foraminiferal DNA due to the association of large numbers of symbionts, commensals and food particles with each foraminifer. The amplification of foraminiferal sequences for the small subunit ribosomal RNA gene is then described, and the phylogenetic placement of the foraminifera within eukaryote evolution examined (papers II and III). Finally, the phylogenetic relationships within the foraminifera are described (paper V).

Diss. (sammanfattning) Stockholm : Stockholms universitet, 2009.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Accepted. Härtill 4 uppsatser.

[EN] In today's information society, there is a growing need to access data communication services ubiquitously, with mobility and increasingly higher data rates. This society's demand has motivated the development of the fourth generation of mobile communications (4G) and its evolution towards the fifth generation (5G). This development has required a revolution on the radio interface of the mobile communications systems, and, consequently, has significantly modified their capabilities and their radio resource management. This is the case of the technology known as Long Term Evolution (LTE) and its 4G version called LTE-Advanced. This Doctoral Thesis addresses the modelling, the radio resource management analysis, and the performance evaluation of the downlink of LTE and LTE-Advanced where, among the different features of LTE-Advanced, the focus is on the Coordinated Multi-Point (CoMP) transmission. The Thesis provides a detailed description of the main characteristics of LTE and LTE-Advanced. The high complexity of these systems, has prompted the use of computer simulations as the primary research methodology. The Thesis makes a detailed description of the simulation methodology and the system modelling required, including some contributions of the author in this field. Among them, it is of significant relevance the link-level simulation results used in the European project WINNER + for the LTE evaluation. With regard to the analysis of the radio resource management in LTE, the fundamentals of link adaptation and scheduling are explained in the first place. In relation to the scheduling, the Thesis includes a thorough study of the proportional fairness concept and the suboptimal implementation typically used in LTE to maximize this metric. This study has resulted in a series of ideas embodied in a modification of the typical implementation, which has proved to be capable of increasing the proportional fairness of the resource allocations. Moreover, the link adaptation analysis has revealed the "flash-light" effect problem, which is characterized by a high interference variability due to rapid changes in the scheduling decisions. The Thesis demonstrates that a particular implementation that stabilizes the scheduling decisions can improve the system performance. The radio resource management analysis of this Thesis is completed with the study of CoMP. Specifically, the CoMP scheme studied in this Thesis is a solution with coordinated scheduling and beamforming (CS/CB), that takes into account realistic and robust assumptions concerning the knowledge that the coordinated points have about the channel state. The Thesis proposes this solution for its simplicity and its ability to improve high data rates coverage and capacity even with incomplete channel knowledge. Concerning LTE and LTE-Advanced evaluation, it is performed in two different types of scenarios. On the one hand, the scenarios defined in the process of evaluation of IMT-Advanced. In this framework, it is evaluated the importance of different multi-antenna techniques, including CoMP, considering full-buffer traffic models. The most important conclusions in these scenarios are the significant performance improvement achieved with spatial multiplexing of users and the fact that CoMP mechanisms provide a reduced benefit. The second group of scenarios are those defined by the European project METIS for the evaluation of 5G technologies. Specifically, an indoor office scenario and an outdoor sports stadium have been selected. In these scenarios, a realistic traffic model is used, and it has been demonstrated the utility of CoMP to satisfy the first 5G requirement definitions with feasible frequency bandwidths. In these scenarios with less homogeneous deployments, or with a limited number of transmitters originating the major part of interference, is where this Thesis has found CoMP to be more useful and where the Thesis promotes its use.
[ES] En la actual sociedad, hay una creciente necesidad de acceso a servicios de comunicación de datos de forma ubicua, móvil y a velocidades cada vez más altas. Esta demanda ha motivado el desarrollo de la cuarta generación de comunicaciones móviles (4G) y su evolución hacia la quinta generación (5G). Este desarrollo ha requerido una revolución en la interfaz radio de los sistemas de comunicaciones móviles modificando en gran medida sus capacidades y la forma en la que se gestionan sus recursos. Este es el caso de la tecnología conocida como Long Term Evolution (LTE) y su versión 4G llamada LTE-Advanced. En concreto, esta Tesis Doctoral aborda el modelado, análisis de la gestión de recursos radio y evaluación de prestaciones del enlace descendente de LTE y LTE-Advanced, donde, de entre las características de LTE-Advanced, se ha puesto el foco de atención en la transmisión multipunto coordinada (CoMP). La Tesis proporciona una descripción detallada de las principales características de LTE y LTE-Advanced. La gran complejidad del sistema descrito ha motivado que la metodología de estudio haya sido la simulación mediante ordenador. La Tesis realiza una descripción detallada de dicha metodología y del modelado del sistema empleado, incluyendo algunas aportaciones del autor en este campo. De entre éstas, destaca la provisión de resultados de simulación de nivel de enlace que se usaron en el proyecto europeo WINNER+ para la evaluación de LTE. En cuanto al análisis de la gestión de recursos radio en LTE, en primer lugar, se explican los fundamentos de la adaptación al enlace y el scheduling. En relación con el scheduling, se realiza un estudio del concepto de proportional fairness y de la implementación subóptima típicamente usada en LTE para maximizar esta métrica. Este estudio ha dado como resultado una modificación de la implementación típica que ha demostrado ser capaz de aumentar la proportional fairness en la asignación de recursos con un bajo incremento de complejidad. Además, el análisis de la adaptación al enlace ha revelado el problema del efecto de "luz de flash" consistente en la alta variabilidad de la interferencia debida a rápidos cambios en las decisiones del scheduler. La Tesis demuestra que se pueden mejorar las prestaciones del sistema estabilizando dichas decisiones mediante una implementación concreta. El bloque de análisis de la gestión de recursos se completa con el estudio de CoMP. Específicamente, se estudia una solución con coordinación de scheduling y conformación de haz (CS/CB) que tiene en cuenta suposiciones reales y robustas en cuanto al conocimiento que los puntos coordinados tienen de los canales radio. La Tesis propone esta solución por su sencillez y capacidad de mejorar la eficiencia de los sistemas de comunicaciones móviles, tanto en cobertura de velocidades altas de transmisión como en capacidad, aun teniendo un conocimiento incompleto del canal. En cuanto a la evaluación de LTE y LTE-Advanced, ésta se realiza en dos tipos de escenarios. Por un lado, los escenarios definidos en el proceso de evaluación de IMT-Advanced. En este marco, se evalúa la importancia de diferentes técnicas de transmisión multiantena, incluyendo CoMP, y considerando tráfico de tipo full-buffer. Se ha obtenido una gran mejora de prestaciones por la multiplexación espacial de usuarios y mejoras discretas por el uso de CoMP. El segundo grupo de escenarios son los definidos por el proyecto europeo METIS para evaluación de tecnologías 5G, concretamente se han elegido un escenario de interiores con una oficina, y uno de exteriores con un estadio deportivo. En estos escenarios se utiliza un tráfico realista y se ha demostrado la utilidad de CoMP para mejorar las prestaciones del sistema. En estos escenarios con despliegues menos uniformes, o con un número limitado de transmisores provocando la mayor parte de la interferencia, es donde esta Tesis ha encontrado la mayor u
[CAT] En l'actual societat de la informació, hi ha una creixent necessitat d'accés a serveis de comunicació de dades de forma ubiqua, mòbil i a velocitats cada vegada més altes. Aquesta demanda de la societat, ha motivat el desenrotllament de la quarta generació de comunicacions mòbils (4G) i la seua evolució cap a la quinta generació (5G). Aquest desenrotllament ha requerit una revolució en la interfície ràdio dels sistemes de comunicacions mòbils i ha modificat en gran manera les seues capacitats i la forma en què es gestionen els seus recursos. Aquest és el cas de la tecnologia coneguda com a Long Term Evolution (LTE) i la seua versió 4G anomenada LTE-Advanced. En concret, aquesta Tesi Doctoral aborda el modelatge, anàlisi de la gestió de recursos ràdio i avaluació de prestacions de l'enllaç descendent de LTE i LTE-Advanced, on, d'entre les característiques de LTE-Advanced, s'ha posat el centre d'atenció en la transmissió multipunt coordinada (CoMP). La Tesi proporciona una descripció detallada de les principals característiques de LTE i LTE-Advanced. La gran complexitat del sistema descrit ha motivat que la metodologia d'estudi s'haja basat en simulació per mitjà d'ordinador. La Tesi realitza una descripció detallada de la metodologia de simulació i del modelatge del sistema empleat, incloent-hi algunes aportacions de l'autor en aquest camp. D'entre aquestes, destaca la provisió de resultats de simulació de nivell d'enllaç que es van usar en el projecte europeu WINNER+ per a l'avaluació de LTE. Pel que fa a l'anàlisi de la gestió de recursos ràdio en LTE, en primer lloc, s'expliquen els fonaments de l'adaptació a l'enllaç i el scheduling. En relació amb el scheduling, es realitza un estudi del concepte de proportional fairness i de la implementació subòptima típicament usada en LTE per a maximitzar aquesta mètrica. L'estudi ha donat com a resultat una modificació de la implementació típica que ha demostrat ser capaç d'augmentar la proportional fairness en l'assignació de recursos amb un baix increment de complexitat. A més, l'anàlisi de l'adaptació a l'enllaç ha desvetllat el problema de l'efecte de "llum de flaix" consistent en la alta variabilitat de la interferència deguda a una ràpida variació de les assignacions de recursos. La Tesi demostra que es poden millorar les prestacions del sistema estabilitzant les decisions del scheduler mitjançant una implementació concreta. En el bloc d'anàlisi de la gestió de recursos d'aquesta Tesi es completa amb l'estudi de CoMP. Específicament, s'estudia una solució amb coordinació de scheduling i conformació de feix (CS/CB), que té en compte suposicions reals i robustes quant al coneixement que els punts coordinats tenen dels canals ràdio dels usuaris servits. La Tesi proposa aquesta solució per la seua senzillesa i capacitat de millorar l'eficiència dels sistemes de comunicacions mòbils, tant en cobertura de velocitats altes de transmissió com en capacitat, encara tenint un coneixement incomplet del canal. Quant a l'avaluació de LTE i LTE-Advanced, aquesta es realitza en dos tipus d'escenaris diferents. D'una banda, els escenaris definits dins del procés d'avaluació de tecnologies IMT-Advanced. Dins d'aquest marc, s'avalua la importància de diferents tècniques de transmissió multi-antena, incloent-hi CoMP, i considerant tràfic de tipus full-buffer. S'ha obtingut una gran millora de prestacions amb la multiplexació espacial d'usuaris i una discreta millora amb CoMP. El segon grup d'escenaris són els definits pel projecte europeu METIS per a l'avaluació de tecnologies 5G, concretament s'han triat un escenari d'interiors amb una oficina, i un d'exteriors amb un estadi esportiu, on s'ha utilitzat un tràfic realista. En aquests escenaris amb desplegaments menys uniformes, o amb un nombre limitat de transmissors provocant la major part de la interferència, és on aquesta Tesi ha trobat la utilitat més gran de
Martín-Sacristán Gandía, D. (2016). 3GPP Long Term Evolution: Performance Analysis and Evolution towards 4G with Coordinated Multi-Point Transmission [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/63261
TESIS

Many software systems eventually undergo changes to their basic architectural structure. Such changes may be prompted by new feature requests, new quality attribute requirements, changing technology, or other reasons. Whatever the causes, architecture evolution is commonplace in real-world software projects. Today’s software architects, however, have few techniques to help them plan such evolution. In particular, they have little assistance in planning alternatives, making trade-offs among these different alternatives, or applying best practices for particular domains. To address this, we have developed an approach for assisting architects in planning and reasoning about software architecture evolution. Our approach is based on modeling and analyzing potential evolution paths that represent different ways of evolving the system. We represent an evolution path as a sequence of transitional architectural states leading from the initial architecture to the target architecture, along with evolution operators that characterize the transitions among these states. We support analysis of evolution paths through the definition and application of constraints that express rules governing the evolution of the systemand evaluation functions that assess path quality. Finally, a set of these modeling elements may be grouped together into an evolution style that encapsulates a body of knowledge relevant to a particular domain of architecture evolution. We evaluate this approach in three ways. First, we evaluate its applicability to real-world architecture evolution projects. This is accomplished through case studies of two very different software organizations. Second, we undertake a formal evaluation of the computational complexity of verifying evolution constraints. Finally, we evaluate the implementability of the approach based on our experiences developing prototype tools for software architecture evolution.

This paper is a content analysis of the "American Archivist," the journal of the "Society of American Archivists." Eight volumes of the journal were analyzed to review the decade by decade thematic and structural evolution of the journal from its foundation in 1938 to the present. Analysis was conducted to determine if the journal had fulfilled its initial requirement “to be as useful as possible to all members of the profession.”

Due to current economic conditions, aircraft are being operated to their design life and often beyond. In order to assess the true condition of these aging aircraft structures, structural teardowns have become more common over the past decade. Teardown data fidelity is highly dependent on the processes developed and implemented to gather the data; therefore, improper procedure selection often results in the destruction or degradation of teardown findings. Incorrect implementation of procedures also occurs during teardown programs and frequently results in increased scatter in the teardown data, which leads to difficulty interpreting the data and applying the results to the fleet. No detailed teardown planning process currently exists that incorporates lessons learned from previous programs. Common problems have occurred in recent teardown programs resulting in increased costs, schedule, and capacity requirements, and likely degradation or destruction of teardown data due to the lack of a defined process. A universally accepted teardown planning process would drastically reduce, or eliminate, these recurring problems. This research provides a step-by-step process for planning and executing a structural teardown program with the goal of minimizing or eliminating problems encountered during past teardown programs. The developed process defines four steps to plan and three steps to execute a structural teardown. Each of these seven steps provides specific recommendations to avoid common pitfalls of previous teardown programs. Four case studies of previous and ongoing teardowns are discussed and the methods implemented are compared to the proposed teardown process to assess potential improvements when using the proposed method. Costs of the proposed process are also compared to costs of the case study teardown programs to weight technical benefit versus increased cost.
Thesis (Ph.D.)--Wichita State University, College of Engineering, Dept. of Aerospace Engineering

Many studies have been conducted regarding network theory and how it can be applied to public transport network. This has led to knowledge on how network indicators relate to the performance of a network and also to insights of how networks can best be extended. Little is known however on how rail bound public transport networks and their network indicators have evolved over time. This would be interesting to know since many metro and other rail bound public transport networks have evolved over a long period of time with extensions being made at different times by different policy makers and stakeholders. This means that there has not been a unified planning process for many of the networks. It would hence be beneficial to get a better picture of how the networks have evolved, when extending the networks or when creating new ones. By creating networks for every year in the development of a rail bound public transport network and then calculate the different network indicators, the evolutionary trends could be found. The networks were created in L-space which means that stations were represented as nodes and the rail connection between stations as edges. To every link in the networks, travel time was attached as weights. This was done in order to make the network indicators more realistic. By assigning geographical coordinates to nodes, indicators such as directness and closeness centrality with respect to geographical distance could be derived. A case study was conducted by applying the methodology to the Stockholm rail bound public transport network. The study period was chosen to be from 1950 up until 2025. 1950 was the year when the Stockholm Metro opened, and the extensions to the network that are decided upon are planned to be completed in 2025. By including the future extensions it was hoped that it could be seen if the future trends are following the trends from the 20th century. Trends regarding the evolution of the network in Stockholm were found. In general it can be said that indicators were relatively high in the first 15-20 years of the study. This was due to the inner city tram network that existed in these years. The tram network was relatively intra-connected with a relatively high average degree, clustering coefficient and connectivity. When the tram network closed down the indicators drastically decreased, after 1971 many of the indicators started to slowly increase due to the additions of new lines and also extensions of already existing ones. Between the year 2000 and 2025, many of the indicators increased substantially, this was partly due to Tvärbanan that connected many older lines creating nodes with a high degree. The fact that the future extensions will lead to an increase in many network indicators (and a decrease in average connectivity) was seen as an indication that the future extensions will accentuate trends that have taken place since the early 1970’s. It was also seen that many of the extensions included in this study will help to develop the network in a way that is in line with the overarching planning principles set by the Stockholm council. The structure of the network consisted of a dense core with branches reaching out to the suburbs in the 1950’s and early 1960’s. In the late 1960’s the network got a radial shape with branches going to the suburbs, no denser core existed in these years. This structure remained relatively unchanged up until the year 2000. After 2000 and up until 2025 a structure emerged in the network with a dense core and also a ring line going around half of the city. This type of structure had been seen in many other rail bound networks around the world.

The purpose of this study is to examine the evolution of six U.S. corporate logos--Apple, McDonald's, Nike, Pepsi, Shell, and Starbucks--from each logo's inception until the newest version of the graphic emblem today. The objective is to determine the meanings that logos have for a corporation's identity, mission, and relationships, as well as the messages that logos convey to viewers (i.e., mostly customers). By "evolution" of logos here, the researcher means "ongoing transformation" of logos. The semiotic model used in this analysis is Charles Sanders Peirce's (1958(1931)) semiotic framework. Peircean semiotics is made up of a three-part paradigm of signification: the representamen (or the sign itself), the object (or "referent"--what the sign refers to), and the interpretant (the effect on the viewer, or the viewer's interpretation). Based on the semiotic data on logo evolution, the researcher found six main themes that emerged across the analyses of U.S. corporate logos. These themes are (1) Direction toward the Future, (2) Identity with Viewers, (3) Instant Recognition and Distinctiveness, (4) Consistency throughout Evolution, (5) Invocation of Change, and (6) True Representation of Corporate Identity. The ultimate conclusion of this analysis is that the communicative intent of a company, through its logo, tends to take a long time to develop. A successful logo is one that portrays the true objectives and principles of a company. For this reason, the ideal identity of a corporation tends to be built over a long period of time, which makes logo improvement "evolutionary" in nature. In all six cases, communication plays a major part in logo improvement.
ID: 029808873; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Thesis (M.A.)--University of Central Florida, 2011.; Includes bibliographical references (p. 87-101).
M.A.
Masters
Communication
Sciences

MBA Professional Report
Soldiers for hire are not a new phenomenon of the twenty-first century. They are as old as war itself. However, in the present day these modern day soldiers for hire are part of well-organized and competently run Private Military Companies (PMC). The private military industry may be one of the most important, but little understood developments in security studies to have taken place over the last decade. This new industry, where firms not only supply the goods of warfare, but also fulfill many of the professional functions, is not only significant to the defense community, but has wider ramifications for global policies and warfare. This study attempts to clarify and analyze the historical evolution of the private military industry, comparing different private military firms and their future impacts on military operations.

This study explores the establishment of the paradigm of evolution by means of natural selection, asserting that Darwin's theories were not scientifically revolutionary because he established rather than overthrew the existing paradigm in biology. Actually Darwin made three more important contributions than the theory of natural selection. He delivered a blow to essentialism, changing the universe from a product into a process. He established the hypothetico-deductive model of the physical sciences for natural history. And he demonstrated that teleological problems could be studied by scientists. The recent controversies in biology are continuations of the old debate over whether evolution is orderly or irregular, controlled by external or internal forces, continuous or discontinuous. The controversies can be separated into four separate challenges to neo-Darwinism: empirical, epistemological, methodological, and teleological. The study concludes that the empirical and teleological challenges do not pose serious threats to the existing paradigm, but unless the epistemological and methodological challenges can be met satisfactorily, the paradigm may be overthrown.This study also explores the differences between the rhetorical and scientific methods of inquiry. Modern science is considered as predominantly empirical, progressing because of the scientists' system of shared, rational values. Actually both metaphysician and physician ponder the same questions, embrace truth with the same assumptions, and operate with the same epistemology. Science is puzzle solving. Rhetoric deals with ill-defined problems, while science turns ill-defined problems into well-defined ones. The danger in separating the scientific and rhetorical methods is that Western man is split into two irreconcilable points of view: the moral and the scientific. The dichotomy arose because of the two fountainheads of Western culture. Plato "solved" the dichotomy by proposing two worlds of Becoming and Ideas. Darwin's solution depends on a different metaphysical pathos which is only now being realized, due to the rethinking of the paradigm as a result of the challenges. Rather than giving us two worlds, Darwin separated the forces of one, completely naturalistic world into a two-step process: chance and necessity. The problem is that many thinkers focus on only one of the processes, sometimes to the exclusion of the other.
Department of English

Thesis (M. Sc.)--University of Sydney, 2008.
Includes tables. Title from title screen (viewed September 19, 2008). Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy to the School of Information Technologies, Faculty of Science. Includes bibliographical references. Also available in print form.

Recent advances in sequencing technology and computing power mean that we are in an unprecedented position to analyse large viral sequence datasets using state-of-the-art methods, with the aim of better understanding pathogen evolution and epidemiology. This thesis concerns the evolutionary analysis of rapidly evolving RNA viruses, with a focus on avian influenza and the use of Bayesian methodologies which account for uncertainty in the evolutionary process. As avian influenza viruses present an epidemiological and economic threat on a global scale, knowledge of how they are circulating and evolving is of substantial public health importance. In the first part of this thesis I consider avian influenza viruses of haemagglutinin (HA) subtype H7 which, along with H5, is the only subtype for which highly pathogenic influenza has been found. I conduct a comprehensive phylogenetic analysis of available H7 HA sequences to reveal global evolutionary relationships, which can help to target influenza surveillance in birds and facilitate the early detection of potential pandemic strains. I provide evidence for the continued distinction between American and Eurasian sequences, and suggest that the most likely route for the introduction of highly pathogenic H5N1 avian influenza to North America would be through the smuggling of caged birds. I proceed to apply novel methods to better understand the evolution of avian influenza. Firstly, I use an extension of stochastic mutational mapping methods to estimate the dN/dS ratio of H7 HA on different neuraminidase (NA) subtype backgrounds. I find dN/dS to be higher on the N2 NA background than on N1, N3 or N7 NA backgrounds, due to differences in selective pressure. Secondly, I investigate reassortment, which generates novel influenza strains and precedes human influenza pandemics. The rate at which reassortment occurs has been difficult to assess, and I take a novel approach to quantifying reassortment across phylogenies using discrete trait mapping methods. I also use discrete trait mapping to investigate inter-subtype recombination in early HIV-1 in Kinshasa, the epicentre of the HIV-1 group M epidemic. In the final section of the thesis, I describe a method whereby epidemiological parameters may be inferred from viral sequence data isolated from different infected individuals in a population. To conclude, I discuss the findings of this thesis in the context of other evolutionary and epidemiological studies, suggest future directions for avian influenza research and highlight scenarios in which the methods described in this thesis might find further application.

The purpose of this research is to help understand the key relationships in an evolving economic structure that are driving resource use and greenhouse gas emissions in Australia. The approach involves looking at the factors and relationships that underpin economic growth in Australia. This research seeks to understand the changes in these factors by taking a historical perspective to the determinants of environmental impact through an investigation of structural changes over a period of 30 years. A detailed model is developed using the macro-economic tool of input-output analysis. This model makes it possible to investigate inter-relationships and intra-relationships between sectors of the environment, the economy and the population at disparate scales.

Doctor of Philosophy (PhD)
The purpose of this research is to help understand the key relationships in an evolving economic structure that are driving resource use and greenhouse gas emissions in Australia. The approach involves looking at the factors and relationships that underpin economic growth in Australia. This research seeks to understand the changes in these factors by taking a historical perspective to the determinants of environmental impact through an investigation of structural changes over a period of 30 years. A detailed model is developed using the macro-economic tool of input-output analysis. This model makes it possible to investigate inter-relationships and intra-relationships between sectors of the environment, the economy and the population at disparate scales.

The aim of this Licentiate Thesis is to discuss special transformations and so-called adjoint symmetries of nonlinear partial differential equations. Nonlinear partial differential equations play an important role in the description of many physical phenomena. In order to understand the phenomena, modelled by the equations mentioned above, it is therefore necessary to obtain and analyze the solutions and the conservation laws of these equations. In this Thesis we investigate some methods to obtain conservation laws and transformations between nonlinear partial differential equations and moreover to classify nonlinear partial differential equations with respect to those methods.The main emphasis is on adjoint symmetries and transformations of evolution equations. In particular we study the adjoint symmetries and the construction of reciprocal Bäcklund transformations for evolution equations.
Godkänd; 2009; 20090115 (lund); Licentiatseminarium för avläggande av teknologie licentiatexamen. Examinator: Docent Marianna Euler, Luleå tekniska universitet Tid: Fredag den 20 mars 2009 kl 10.15 Plats: D2222, Luleå tekniska universitet

Fungi is the eukaryotic group with a largest amount of completely sequenced species and therefore it is particularly well suited for comparative genomics analyses.
A species tree is often an important part of phylogenomics analysis. Concern about its reliability led us to design several methods by which we could identify nodes in the species tree that were poorly supported by a whole phylome. We determined that the species tree was mostly well supported but some nodes showed large discrepancies to most genes.
These results could partly be attributed to evolutionary events that result in topological changes in gene trees. Our analyses have shown that HGT plays an important role in fungal evolution. Gene duplications followed by differential loss are also often the cause of incongruence. The OXPHOS pathway, despite being formed by multi-protein complexes, has been affected by this process at similar levels than the rest of the genome.
Els fongs són el grup d'espècies eucariotes amb un major nombre de genomes completament seqüenciats. Per això són un grup ideal on aplicar tècniques filogenòmiques.
L'arbre de les espècies és un punt clau en molts anàlisis filogenòmics i com a tal necessitem saber si és fiable. Hem dissenyat diferents mesures que aprofiten la informació d'un filoma per identificar aquells punts en l'arbre de les especies que no estan ben suportats. Les discrepàncies que hem trobat poden ser degudes a successos evolutius (transferència horitzontal, duplicacions,...). Hem demostrat que la transferència horitzontal juga un paper important en l'evolució de fongs. També hem estudiat els efectes de duplicacions en l'evolució de la via metabòlica de la fosforilació oxidativa.
Podem concloure que l'arbre de les especies és majoritàriament robust, però que necessitem ser capaços d'identificar nodes subjectes a variacions. Successos evolutius poden ser la causa de les discrepàncies observades en els arbres gènics.

Evolution of enzymes with novel functional properties has gained much attention in recent years. Naturally evolved enzymes are adapted to work in living cells under physiological conditions, circumstances that are not always available for industrial processes calling for novel and better catalysts. Furthermore, altering enzyme function also affords insight into how enzymes work and how natural evolution operates.

Previous investigations have explored catalytic properties in the directed evolution of mutant libraries with high sequence variation. Before this study was initiated, functional analysis of mutant libraries was, to a large extent, restricted to uni- or bivariate methods. Consequently, there was a need to apply multivariate data analysis (MVA) techniques in this context. Directed evolution was approached by DNA shuffling of glutathione transferases (GSTs) in this thesis. GSTs are multifarious enzymes that have detoxication of both exo- and endogenous compounds as their primary function. They catalyze the nucleophilic attack by the tripeptide glutathione on many different electrophilic substrates.

Several multivariate analysis tools, e.g. principal component (PC), hierarchical cluster, and K-means cluster analyses, were applied to large mutant libraries assayed with a battery of GST substrates. By this approach, evolvable units (quasi-species) fit for further evolution were identified. It was clear that different substrates undergoing different kinds of chemical transformation can group together in a multi-dimensional substrate-activity space, thus being responsible for a certain quasi-species cluster. Furthermore, the importance of the chemical environment, or substrate matrix, in enzyme evolution was recognized. Diverging substrate selectivity profiles among homologous enzymes acting on substrates performing the same kind of chemistry were identified by MVA. Important structure-function activity relationships with the prodrug azathioprine were elucidated by segment analysis of a shuffled GST mutant library. Together, these results illustrate important methods applied to molecular enzyme evolution.