Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes

Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process.

Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions.

BACKGROUND: Recent methodological advances allow better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing frameworks to model this diversity either focus on changes between lineages, neglecting global effects such as mass extinctions, or focus on changes over time which would affect all lineages. Yet it seems probable that both lineages differences and mass extinctions affect the same groups. RESULTS: Here we used simulations to test the performance of two widely used methods under complex scenarios of diversification. We report good performances, although with a tendency to over-predict events with increasing complexity of the scenario. CONCLUSION: Overall, we find that lineage shifts are better detected than mass extinctions. This work has significance to assess the methods currently used to estimate changes in diversification using phylogenetic trees. Our results also point toward the need to develop new models of diversification to expand our capabilities to analyse realistic and complex evolutionary scenarios.

Continental faunal exchange and the asymmetrical radiation of carnivores.

Lineages arriving on islands may undergo explosive evolutionary radiations owing to the wealth of ecological opportunities. Although studies on insular taxa have improved our understanding of macroevolutionary phenomena, we know little about the macroevolutionary dynamics of continental exchanges. Here we study the evolution of eight Carnivora families that have migrated across the Northern Hemisphere to investigate if continental invasions also result in explosive diversification dynamics. We used a Bayesian approach to estimate speciation and extinction rates from a substantial dataset of fossil occurrences while accounting for the incompleteness of the fossil record. Our analyses revealed a strongly asymmetrical pattern in which North American lineages invading Eurasia underwent explosive radiations, whereas lineages invading North America maintained uniform diversification dynamics. These invasions into Eurasia were characterized by high rates of speciation and extinction. The radiation of the arriving lineages in Eurasia coincide with the decline of established lineages or phases of climate change, suggesting differences in the ecological settings between the continents may be responsible for the disparity in diversification dynamics. These results reveal long-term outcomes of biological invasions and show that the importance of explosive radiations in shaping diversity extends beyond insular systems and have significant impact at continental scales.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Empirical study on the adoption, use and effects of cloud-based testing

Cloud computing is a practically relevant paradigm in computing today. Testing is one of the distinct areas where cloud computing can be applied. This study addressed the applicability of cloud computing for testing within organizational and strategic contexts. The study focused on issues related to the adoption, use and effects of cloudbased testing. The study applied empirical research methods. The data was collected through interviews with practitioners from 30 organizations and was analysed using the grounded theory method. The research process consisted of four phases. The first phase studied the definitions and perceptions related to cloud-based testing. The second phase observed cloud-based testing in real-life practice. The third phase analysed quality in the context of cloud application development. The fourth phase studied the applicability of cloud computing in the gaming industry. The results showed that cloud computing is relevant and applicable for testing and application development, as well as other areas, e.g., game development. The research identified the benefits, challenges, requirements and effects of cloud-based testing; and formulated a roadmap and strategy for adopting cloud-based testing. The study also explored quality issues in cloud application development. As a special case, the research included a study on applicability of cloud computing in game development. The results can be used by companies to enhance the processes for managing cloudbased testing, evaluating practical cloud-based testing work and assessing the appropriateness of cloud-based testing for specific testing needs.

Cloud computing contribution to manufacturing industry

Manufacturing industry has been always facing challenge to improve the production efficiency, product quality, innovation ability and struggling to adopt cost-effective manufacturing system. In recent years cloud computing is emerging as one of the major enablers for the manufacturing industry. Combining the emerged cloud computing and other advanced manufacturing technologies such as Internet of Things, service-oriented architecture (SOA), networked manufacturing (NM) and manufacturing grid (MGrid), with existing manufacturing models and enterprise information technologies, a new paradigm called cloud manufacturing is proposed by the recent literature. This study presents concepts and ideas of cloud computing and cloud manufacturing. The concept, architecture, core enabling technologies, and typical characteristics of cloud manufacturing are discussed, as well as the difference and relationship between cloud computing and cloud manufacturing. The research is based on mixed qualitative and quantitative methods, and a case study. The case is a prototype of cloud manufacturing solution, which is software platform cooperated by ATR Soft Oy and SW Company China office. This study tries to understand the practical impacts and challenges that are derived from cloud manufacturing. The main conclusion of this study is that cloud manufacturing is an approach to achieve the transformation from traditional production-oriented manufacturing to next generation service-oriented manufacturing. Many manufacturing enterprises are already using a form of cloud computing in their existing network infrastructure to increase flexibility of its supply chain, reduce resources consumption, the study finds out the shift from cloud computing to cloud manufacturing is feasible. Meanwhile, the study points out the related theory, methodology and application of cloud manufacturing system are far from maturity, it is still an open field where many new technologies need to be studied.

Properties and algorithms of the (n, k)-arrangement graphs

The (n, k)-arrangement interconnection topology was first introduced in 1992. The (n, k )-arrangement graph is a class of generalized star graphs. Compared with the well known n-star, the (n, k )-arrangement graph is more flexible in degree and diameter. However, there are few algorithms designed for the (n, k)-arrangement graph up to present. In this thesis, we will focus on finding graph theoretical properties of the (n, k)- arrangement graph and developing parallel algorithms that run on this network. The topological properties of the arrangement graph are first studied. They include the cyclic properties. We then study the problems of communication: broadcasting and routing. Embedding problems are also studied later on. These are very useful to develop efficient algorithms on this network. We then study the (n, k )-arrangement network from the algorithmic point of view. Specifically, we will investigate both fundamental and application algorithms such as prefix sums computation, sorting, merging and basic geometry computation: finding convex hull on the (n, k )-arrangement graph. A literature review of the state-of-the-art in relation to the (n, k)-arrangement network is also provided, as well as some open problems in this area.

Lighting recommendations for the Ryan Electric Scintillator and Fireworks Program for the official dedication Niagara Falls illumination, 1925

Walter D’Arcy Ryan was born in 1870 in Kentville, Nova Scotia. He became the chief of the department of illumination at the General Electric Company of Schenectady, New York. He was a founder in the field of electrical illumination. He built the electric steam scintillator which had numerous nozzles and valves. The operator would release steam through the valves. The nozzles all had names which included: Niagara, fan, snake, plume, column, pinwheel and sunburst. The steam scintillator was combined with projectors, prismatic reflectors, flashers and filters to produce the desired effects. In 1920 a group of businessmen from Niagara Falls, New York formed a group who called themselves the “generators’. They lobbied the American and Canadian governments to improve the illumination of the Falls. They were able to raise $58, 000 for the purchase and installation of 24 arc lights to illuminate the Falls. On February 24th, 1925 the Niagara Falls Illumination Board was formed. Initially, the board had a budget of $28,000 for management, operation and maintenance of the lights. The power was supplied free by the Ontario Power Company. They had 24 lights installed in a row on the Ontario Power Company surge tank which was next to the Refectory in Victoria Park on the Canadian side. The official opening ceremony took place on June 8th, 1925 and included a light parade in Niagara Falls, New York and an international ceremony held in the middle of the Upper Steel Arch Bridge. Walter D’Arcy Ryan was the illuminating engineer and A.D. Dickerson who was his New York field assistant directed the scintillator. with information from American Technological Sublime by David E. Nye and the Niagara Falls info website Location: Brock University Archives Source Information: Subject Headings: Added Entries: 100 Ryan, W. D’A. |q (Walter D’Arcy), |d 1870-1934 610 General Electric Company 650 Lighting, Architectural and decorative 650 Lighting |z New York (State) |z Niagara Falls 700 Dickerson, A.F. 700 Schaffer, J.W. Related material held at other repositories: The Niagara Falls Museum in Niagara Falls, Ontario has a program (pamphlet) dedicating new lighting in 1958 and it has postcards depicting the illumination of the Falls. Some of Ryan’s accomplishments can be seen at The Virtual Museum of the City of San Francisco. Described by: Anne Adams Date: Sept 26,Upper Steel Arch Bridge. Walter D’Arcy Ryan was the illuminating engineer and A.D. Dickerson who was his New York field assistant directed the scintillator. with information from American Technological Sublime by David E. Nye and the Niagara Falls info website

Population Ethics and the Value of Life

Public policies often involve choices of alternatives in which the size and the composition of the population may vary. Examples are the allocation of resources to prenatal care and the design of aid packages to developing countries. In order to assess the corresponding feasible choices on normative grounds, criteria for social evaluation that are capable of performing variable-population comparisons are required. We review several important axioms for welfarist population principles and discuss the link between individual well-being and the desirability of adding a new person to a given society.

Tribunals and Guidelines: Exploring the Relationship Between Fairness and Legitimacy in Administrative Decision-Making

Un résumé en français est également disponible.

Temporalité et surveillance dans l'art de David Rokeby

Pour respecter les droits d'auteur, la version électronique de ce mémoire à été dépouillée de ses documents visuels et audio-visuels. La version intégrale du mémoire a été déposée au Service de la gestion des documents et des archives de l'Université de Montréal.

Des typologies mécaniques à l'expérience esthétique : fonctions et mutations du genre dans le jeu vidéo

Cette thèse examine en profondeur la nature et l’application du concept de genre en jeu vidéo. Elle se divise en trois parties. La première fait l’inventaire des théories des genres en littérature et en études cinématographiques. Les propriétés essentielles du genre comme concept sont identifiées : il s’agit d’une catégorisation intuitive et irraisonnée, de nature discursive, qui découle d’un consensus culturel commun plutôt que de systèmes théoriques, et qui repose sur les notions de tradition, d’innovation et d’hybridité. Dans la deuxième partie, ces constats sont appliqués au cas du genre vidéoludique. Quelques typologies sont décortiquées pour montrer l’impossibilité d’une classification autoritaire. Un modèle du développement des genres est avancé, lequel s’appuie sur trois modalités : l’imitation, la réitération et l’innovation. Par l’examen de l’histoire du genre du first-person shooter, la conception traditionnelle du genre vidéoludique basée sur des mécanismes formels est remplacée par une nouvelle définition centrée sur l’expérience du joueur. La troisième partie développe l’expérience comme concept théorique et la place au centre d’une nouvelle conception du genre, la pragmatique des effets génériques. Dans cette optique, tout objet est une suite d’amorces génériques, d’effets en puissance qui peuvent se réaliser pourvu que le joueur dispose des compétences génériques nécessaires pour les reconnaître. Cette nouvelle approche est démontrée à travers une étude approfondie d’un genre vidéoludique : le survival horror. Cette étude de cas témoigne de l’applicabilité plus large de la pragmatique des effets génériques, et de la récursivité des questions de genre entre le jeu vidéo, la littérature et le cinéma.

Les fondements de la désobéissance civile

Ce mémoire sur les fondements de la désobéissance civile se divise en trois parties. Le premier chapitre concerne la définition de la désobéissance civile d’après l’analyse d’Hugo Adam Bedau. Le deuxième chapitre traite des origines historiques du concept à partir des textes de David Henry Thoreau et Léon Tolstoï jusqu’aux campagnes de Mohandas Gandhi et Martin Luther King. Le dernier chapitre porte sur la pratique de la désobéissance civile dans les régimes démocratiques selon John Rawls. L’objectif de ce mémoire est de démontrer que la désobéissance civile est conforme à la justice malgré son caractère illégal, qu’elle a été bénéfique historiquement à l’évolution des mentalités et qu’elle est nécessaire en démocratie.

Topological Invariants in Hydrodynamics and Hydromagnetics

In this thesis we are studying possible invariants in hydrodynamics and hydromagnetics. The concept of flux preservation and line preservation of vector fields, especially vorticity vector fields, have been studied from the very beginning of the study of fluid mechanics by Helmholtz and others. In ideal magnetohydrodynamic flows the magnetic fields satisfy the same conservation laws as that of vorticity field in ideal hydrodynamic flows. Apart from these there are many other fields also in ideal hydrodynamic and magnetohydrodynamic flows which preserves flux across a surface or whose vector lines are preserved. A general study using this analogy had not been made for a long time. Moreover there are other physical quantities which are also invariant under the flow, such as Ertel invariant. Using the calculus of differential forms Tur and Yanovsky classified the possible invariants in hydrodynamics. This mathematical abstraction of physical quantities to topological objects is needed for an elegant and complete analysis of invariants.Many authors used a four dimensional space-time manifold for analysing fluid flows. We have also used such a space-time manifold in obtaining invariants in the usual three dimensional flows.In chapter one we have discussed the invariants related to vorticity field using vorticity field two form w2 in E4. Corresponding to the invariance of four form w2 ^ w2 we have got the invariance of the quantity E. w. We have shown that in an isentropic flow this quantity is an invariant over an arbitrary volume.In chapter three we have extended this method to any divergence-free frozen-in field. In a four dimensional space-time manifold we have defined a closed differential two form and its potential one from corresponding to such a frozen-in field. Using this potential one form w1 , it is possible to define the forms dw1 , w1 ^ dw1 and dw1 ^ dw1 . Corresponding to the invariance of the four form we have got an additional invariant in the usual hydrodynamic flows, which can not be obtained by considering three dimensional space.In chapter four we have classified the possible integral invariants associated with the physical quantities which can be expressed using one form or two form in a three dimensional flow. After deriving some general results which hold for an arbitrary dimensional manifold we have illustrated them in the context of flows in three dimensional Euclidean space JR3. If the Lie derivative of a differential p-form w is not vanishing,then the surface integral of w over all p-surfaces need not be constant of flow. Even then there exist some special p-surfaces over which the integral is a constant of motion, if the Lie derivative of w satisfies certain conditions. Such surfaces can be utilised for investigating the qualitative properties of a flow in the absence of invariance over all p-surfaces. We have also discussed the conditions for line preservation and surface preservation of vector fields. We see that the surface preservation need not imply the line preservation. We have given some examples which illustrate the above results. The study given in this thesis is a continuation of that started by Vedan et.el. As mentioned earlier, they have used a four dimensional space-time manifold to obtain invariants of flow from variational formulation and application of Noether's theorem. This was from the point of view of hydrodynamic stability studies using Arnold's method. The use of a four dimensional manifold has great significance in the study of knots and links. In the context of hydrodynamics, helicity is a measure of knottedness of vortex lines. We are interested in the use of differential forms in E4 in the study of vortex knots and links. The knowledge of surface invariants given in chapter 4 may also be utilised for the analysis of vortex and magnetic reconnections.