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The challenge in finding genes in eukaryotic organisms using computational methods is an ongoing problem in the biology. Based on various genomic signals found in eukaryotic genomes, this problem can be divided into many different sub­-problems such as identification of transcription start sites, translation initiation sites, splice sites, poly (A) signals, etc. Each sub-­problem deals with a particular type of genomic signals and various computational methods are used to solve each sub-­problem. Aggregating information from all these individual sub-­problems can lead to a complete annotation of a gene and its component signals. The fundamental principle of most of these computational methods is the mapping principle – building an input-­output model for the prediction of a particular genomic signal based on a set of known input signals and their corresponding output signal. The type of input signals used to build the model is an essential element in most of these computational methods. The common factor of most of these methods is that they are mainly based on the statistical analysis of the basic nucleotide sequence string composition. 4 Our study is based on a novel approach to predict genomic signals in which uniquely generated structural profiles that combine compressed physicochemical properties with topological and compositional properties of DNA sequences are used to develop machine learning predictive models. The compression of the physicochemical properties is made using principal component analysis transformation. Our ideas are evaluated through prediction models of canonical splice sites using support vector machine models. We demonstrate across several species that the proposed methodology has resulted in the most accurate splice site predictors that are publicly available or described. We believe that the approach in this study is quite general and has various applications in other biological modeling problems.

Polish composer Witold Lutos?awski (1913-1994) was one of the most representative composers of the twentieth-century. Lutos?awski’s style progressed from traditional to modern avant-garde. His Piano Sonata belongs to his first compositional period, and is the only extant work from his student years. His remarkable synthesis of classical structures and impressionistic harmonic sonorities distinguishes the Sonata. Lutos?awski’s Piano Sonata is divided into three movements, and each movement is written in traditional sonata allegro form, sonata form without development and modified sonata form respectively. The Sonata contains both considerable elements of Classicism and Impressionism, as well as traits of Post-romanticism and Neoclassicism. The evolution of Lutos?awski’s compositional language can be better understood through an in-depth study of his Piano Sonata. Although Lutos?awski did not allow the work to be published during his lifetime, this occurred posthumously, ten years after the composer´s death. The recent publication of the work, paired with its substantial technical demands, both account for the fact that the Sonata is not frequently performed. The complex textures of Sonata place extensive technical and musical demands on the performer. In this study, a detailed description of the composer´s early style and influences as relates to this work will be analyzed and technical and pianistic approaches necessary for a performance of the work will be addressed. Also, there are significant discrepancies between the manuscript and printed score, even though the edition is based on the manuscript. Only one manuscript survives and scholarly research involving the work is scarce. Discrepancies between the manuscript and the published edition will be detailed, with suggestions for performance. It is hoped that this study will provide interest and be conducive to better approach the performance of this Piano Sonata.

The mathematical model that has been recognized to have the more accurate approximation to the physical laws govern subsurface hydrocarbon flow in reservoirs is the Compositional Model. The features of this model are adequate to describe not only the performance of a multiphase system but also to represent the transport of chemical species in a porous medium. Its importance relies not only on its current relevance to simulate petroleum extraction processes, such as, Primary, Secondary, and Enhanced Oil Recovery Process (EOR) processes but also, in the recent years, carbon dioxide (CO2) sequestration. The purpose of this study is to investigate the subsurface compositional flow under isothermal conditions for several oil well cases. While simultaneously addressing computational implementation finesses to contribute to the efficiency of the algorithm. This study provides the theoretical framework and computational implementation subtleties of an IMplicit Pressure Explicit Composition (IMPEC)-Volume-balance (VB), two-phase, equation-of-state, approach to model isothermal compositional flow based on the finite difference scheme. The developed model neglects capillary effects and diffusion. From the phase equilibrium premise, the model accounts for volumetric performances of the phases, compressibility of the phases, and composition-dependent viscosities. The Equation of State (EoS) employed to approximate the hydrocarbons behaviour is the Peng Robinson Equation of State (PR-EOS). Various numerical examples were simulated. The numerical results captured the complex physics involved, i.e., compositional, gravitational, phase-splitting, viscosity and relative permeability effects. Regarding the numerical scheme, a phase-volumetric-flux estimation eases the calculation of phase velocities by naturally fitting to phase-upstream-upwinding. And contributes to a faster computation and an efficient programming development.

In this bachelor thesis in the field of artistic research, the author’s aim was to gain practical and experience-based knowledge on how to access their inner voice in the process of composing notated contemporary music. The theoretical framework was obtained from theories on compositional craft, composers’ voice and a concept from the rhetoric, mimesis, was used as a model for the approach to creating composition exercises. The procedure of the bachelor thesis started with semi-structured interviews with four professional composers, who were asked about their compositional processes. Based on the results of the interviews, a composition exercise, called mimesis-exercise, was created for each of the interviewee, and then performed by the author. After each mimesis-exercise was finished, a reflective evaluation on the process was written.  A summary of each interview is presented in the implementation and detailed descriptions on how the compositional process was conducted for each of the four mimesis-exercises are presented in the results part. The artistic production of the bachelor thesis consists of five new pieces, each composed for one of the ensembles: SATB-choir, string ensemble, organ (two pieces), and solo trombone. The four research questions were answered through a thematic analysis and reflective texts.   The conclusions made during the process of the bachelor thesis was that the author experienced an enhanced understanding and connection to both the compositional process and the sounding material produced. The experience of composing, both the pieces which was part of the project, but especially those composed close after the thesis’s end, was more emotional and personal than the author experienced before the start of the bachelor thesis. The author reflected on how her development and discovering of her compositional voice was made through the procedure of the mimesis-exercises. The conclusive texts of the bachelor thesis add accounts for experience-based and personal perspectives to previous research on composer’s voice.

L’objectif de cette thèse CIFRE, réalisée avec la société d’études de marché BVA en collaboration avec le constructeur automobile Renault, est de mesurer l’impact des investissements media pour différents canaux (télévision, affichage, etc.) sur les parts de marché de différentes marques, en prenant en compte la concurrence et les potentiels effets croisés et synergies entre ces marques, ainsi qu’en tenant compte du prix des véhicules, du contexte réglementaire (i.e. prime à la casse), et des effets retard de la publicité.Nous avons puisé dans les littératures marketing et statistique pour développer, comparer et interpréter plusieurs modèles qui respectent la contrainte de somme unitaire des parts de marché. Une application concrète au marché automobile français est présentée, pour laquelle nous montrons que les parts de marché des marques sont plus ou moins sensibles aux investissements publicitaires consentis dans chaque canal, et qu’il existe de synergies entre certaines marques. / The aim of this CIFRE thesis, realized with the market research institute BVA in collaboration with the automobile manufacturer Renault, is to build a model in order to measure the impact of media investments of several channels (television, outdoor, etc.) on the brands’ market shares, taking into account the competition and the potential cross effects and synergies between brands, as well as accounting for the price, the regulatory context (scrapping incentive), and the lagged effects of advertising. We have drawn from marketing and statistical literatures to develop, compare and interpret several models which respect the unit sum constraint of market shares. A practical application to the French automobile market is presented, for which it is shown that brands’ market shares are more or less sensitive to advertising investments made in each channel, and that synergies between brands exist.

Este trabalho consiste em dois volumes, sendo o primeiro um memorial de composição e o segundo a partitura e gravação do Septeto - para cordas, piano e acordeom, peça que foi composta no segundo ano do curso de mestrado. O memorial inicia com breve comentário sobre o processo de composição e aspectos técnicos do Quinteto para cordas e piano, composição desenvolvida no curso de mestrado durante o primeiro ano e relevante para a posterior composição do Septeto. Relativo ao Septeto, são abordados o planejamento de sua da forma e conteúdo expressivo, seguido da descrição e comentários a respeito do processo de composição de cada movimento. O memorial passa então a uma seção mais analítica que tem como objetivo demonstrar recursos usados na busca de identidade expressiva de cada movimento e de unidade para o todo. Essa análise trata dos desafios e soluções referentes às conexões dos diversos materiais encontrados na música, dos critérios para a organização das alturas, da orquestração, do uso do ritmo e métrica, bem como das referências musicais que estimularam o processo criativo. Ao final é feita uma avaliação crítica do processo composicional e dos resultados alcançados. / The Septet for strings, piano and accordion was composed during the second year of my master’s course and consists of seven movements, with a total duration time of 53 minutes. The volume I of this paper will present and analyze the composition of the Septet and the volume II present the scoring and record of thenpiece. This paper starts with a brief commentary about the composition process and technical aspects of the Quintet for strings and piano, a piece created during my first year of the master’s course and relevant to the later composition of the Septet. Concerning the Septet, it will be addressed the planning of its form and its expressive content, followed by a description and commentary of each movement’s composition process. After that, this project will analyze the resources used in the pursue of the expressive identity of each movement and the pursue of a sense of unity for the whole piece. The analysis addresses the challenges and solutions found in the process of connecting the diverse nature of the different movements, as well as discuss the criteria used for determining the pitch structure, orchestration, use of rhythm and metrics, and musical references that stimulated the creative process. At the end, a critical evaluation of the compositional process and the achieved results will be made.

It has been known that volatile oil and gas condensate reservoirs cannot be modeled accurately with conventional black-oil models. One variation to the black-oil approach is the modified black-oil (MBO) model that allows the use of a simple, and less expensive computational algorithm than a fully compositional model that can result in significant timesaving in full field studies. The MBO model was tested against the fully compositional model and performances of both models were compared using various production and injection scenarios for a rich gas condensate reservoir. The software used to perform the compositional and MBO runs were Eclipse 300 and Eclipse 100 versions 2002A. The effects of black-oil PVT table generation methods, uniform composition and compositional gradient with depth, initialization methods, location of the completions, production and injection rates, kv/kh ratios on the performance of the MBO model were investigated. Vertical wells and horizontal wells with different drain hole lengths were used. Contrary to the common belief that oil-gas ratio versus depth initialization gives better representation of original fluids in place, initializations with saturation pressure versus depth gave closer original fluids in place considering the true initial fluids in place are given by the fully compositional model initialized with compositional gradient. Compared to the compositional model, results showed that initially there was a discrepancy in saturation pressures with depth in the MBO model whether it was initialized with solution gas-oil ratio (GOR) and oil-gas ratio (OGR) or dew point pressure versus depth tables. In the MBO model this discrepancy resulted in earlier condensation and lower oil production rates than compositional model at the beginning of the simulation. Unrealistic vaporization in the MBO model was encountered in both natural depletion and cycling cases. Oil saturation profiles illustrated the differences in condensate saturation distribution for the near wellbore area and the entire reservoir even though the production performance of the models was in good agreement. The MBO model representation of compositional phenomena for a gas condensate reservoir proved to be successful in the following cases: full pressure maintenance, reduced vertical communication, vertical well with upper completions, and producer set as a horizontal well.

Formal verification techniques have been widely deployed as means to ensure the quality of software products. Unfortunately, they suffer with the combinatorial explosion of the state space. That is, programs have a large number of states, sometimes infinite. A common approach to alleviate the problem is to perform the verification over abstract models from the program. Control-flow graphs (CFG) are one of the most common models, and have been widely studied in the past decades. Unfortunately, previous works over modern programming languages, such as Java, have either neglected features that influence the control-flow, or do not provide a correctness argument about the CFG construction. This is an unbearable issue for formal verification, where soundness of CFGs is a mandatory condition for the verification of safety-critical properties. Moreover, one may want to extract CFGs from the available components of an open system. I.e., a system whose at least one of the components is missing. Soundness is even harder to achieve in this scenario, because of the unknown inter-dependences between software components. In the current work we present a framework to extract control-flow graphs from open Java Bytecode systems in a modular fashion. Our strategy requires the user to provide interfaces for the missing components. First, we present a formal definition of open Java bytecode systems. Next, we generalize a previous algorithm that performs the extraction of CFGs for closed programs to a modular set-up. The algorithm uses the user-provided interfaces to resolve inter-dependences involving missing components. Eventually the missing components will arrive, and the open system will become closed, and can execute. However, the arrival of a component may affect the soundness of CFGs which have been extracted previously. Thus, we define a refinement relation, which is a set of constraints upon the arrival of components, and prove that the relation guarantees the soundness of CFGs extracted with the modular algorithm. Therefore, the control-flow safety properties verified over the original CFGs still hold in the refined model. We implemented the modular extraction framework in the ConFlEx tool. Also, we have implemented the reusage from previous extractions, to enable the incremental extraction of a newly arrived component. Our technique performs substantial over-approximations to achieve soundness. Despite this, our test cases show that ConFlEx is efficient. Also, the extraction of the CFGs gets considerable speed-up by reusing results from previous analyses. / <p>QC 20121029</p> / Verification of Control-Flow Properties of Programs with Procedures(CVPP)

Since the plus fraction of reservoir fluids has some uncertainty in its molecular weight and critical properties, equation-of-state, EOS, are generally not predictive without tuning its parameters to match experimental data. Tuning of the EOS is found to be the best method for improving the predictions of compositional reservoir simulators. The proposed strategy for tuning EOS consists of seven steps: (1) split the laboratory plus fraction to single carbon number groups, SCN, usually up to SCN 44; the last component will be C45+, (2) use set of correlations to calculate the critical properties and acentric factor for each SCN group, (3) match the saturation pressure at reservoir temperature by altering the measured value of the molecular weight of the plus fraction using the extended composition, (4) group SCN groups to multiple carbon number groups, MCN, (5) assign critical properties and acentric factor for each MCN group, (6) rematch the saturation pressure at reservoir temperature using the grouped composition, and (7) match the volumetric data by regressing on volume shift parameters of all components in grouped composition. This research shows an accurate method to split the plus fraction to SCN groups. The most accurate set of correlations to calculate the critical properties and acentric factor for each SCN group that will result in a small adjustment for the molecular weight of the plus fraction when saturation pressure is matched using the extended composition. The proposed strategy groups the extended composition to eight pseudocomponents. The binary interaction coefficients between hydrocarbons and between hydrocarbons and non-hydrocarbons are set to zero which dramatically reduces the simulation time. The strategy proposed in this research for tuning EOS to match experimental data has been tested for a wide range of C7+ mole% (4 – 25) which covers gas condensate and volatile oil samples. Also, using this strategy to tune EOS at reservoir temperature will accurately predict the fluid properties at separator conditions and saturation pressures at different temperatures. The scope of this research is to come up with an accurate and systematic technique for tuning an EOS for use in compositional simulation.