Systèmes-de-systèmes (Systems-of-Systems, SoS) sont des systèmes à logiciel prépondérant de grande échelle, complexes et souvent critiques dont l’importance n’a cessé de croître dans cette décennie. C’est le cas, par exemple, des SoS pour les réseaux intelligents d’énergie, les transports multimodaux et les villes intelligentes. On retrouve les SoS dans des domaines d’application très variés tels que l’environnement, le transport, l’énergie, la santé, l’aérospatiale, l’aéronautique et l’automobile. Pour maîtriser la complexité de tels systèmes évolutionnaires à logiciel prépondérant, il est fondamental de pouvoir concevoir leurs architectures logicielles afin de satisfaire leurs exigences fonctionnelles et non-fonctionnelles. En particulier, il est nécessaire de modéliser et exécuter des processus systématiques pour concevoir les architectures logicielles de SoS. Malgré ce besoin croissant, la plupart de leurs architectures logicielles sont encore développées de manière ad hoc. En général, il y a un manque de processus structurés pour concevoir les architectures des SoS. Cet état de l’art entrave leur développement, notamment pour les applications critiques. Cette thèse présente SOAR (General Process for Acknowledged SoS Software Architectures) qui rend possible la mise en place de processus de conception architecturale pour SoS reconnus. Ce framework de processus a été conçu pour fournir différents niveaux de support en fonction des différents contextes de développement de SoS. Il comprend un noyau de haut niveau qui décrit ce qu’il faut faire pour la conception des architectures de SoS et ainsi que trois pratiques avec des activités spécifiques et des produits de travail pour guider l’analyse, la synthèse et l’évaluation architecturale. SOAR a été implémenté à l’aide d’Essence (Kernel and Language for Software Engineering Methods), un Standard OMG/SEMAT. Afin de valider SOAR, trois enquêtes, une étude de viabilité et une expérimentation ont été menées. Les résultats obtenus dans ces trois études montrent que SOAR répond positivement au besoin exprimée. / System-of-Systems (SoS) refer to complex, large-scale, and often critical software-intensive systems whose importance has rapidly grown over this decade. This is the case, for instance, of SoS for energy grids, multimodal traffic control, and smart cities. We find SoS in different application areas as diverse as environment, transportation, energy, healthcare, aerospace, aeronautics, and automotive. For mastering the complexity of such evolutionary software-intensive systems, it is fundamental to be able to design their software architectures for satisfying both functional and non-functional requirements. In particular, there is the need to model and enact systematic processes to design SoS software architectures. Despite this increasing necessity, most of the SoS software architectures have been still developed in an ad hoc manner. In general, there is a lack of structured processes for architecting SoS. This state-of-art hinders SoS development, in particular for critical applications. This thesis presents SOAR (General Process for Acknowledged SoS Software Architectures) that supports the modeling and enactment of architectural design processes for acknowledged SoS. Conceived to provide different levels of support according to different SoS development contexts, it comprises a high-level kernel that describes what must be done when architecting SoS and also three practices with specific activities and work products to guide how to perform architectural analysis, synthesis, and evaluation. SOAR was implemented using Essence (Kernel and Language for Software Engineering Methods), an OMG/SEMAT Standard. To validate SOAR, three surveys, a viability study, and an experiment were conducted. Results achieved in these studies indicate that SOAR positively meets the expressed need.

Under mina fyra år som gymnasielärare har jag hunnit gå många kurser i nätverksoperativsystemsanvändning. Dessa kurser har varit utformade av de största tillverkarna av nätverksoperativsystem på marknaden och innehållit både föreläsningar och laborationer. Det som slagit mig under dessa kurser, är att jag sällan kommit ihåg det jag laborerat om. Eller rättare sagt, jag kommer ihåg att jag laborerat om det, men inte hur man gjorde. Så skulle någon be mig upprepa uppgifterna eller lösa liknande uppgifter så skulle jag troligen inte klara av det. Effekten av detta är att jag ser dessa kurser som bra inspiration och inledning till att lära mig något nytt, men inte som ett sätt att lära mig något. Jag hävdar absolut inte att dessa kurser är dåliga, då de är gjorda för att gå igenom en väldigt stor kunskapsmängd på en vecka. Samma kunskapsmängd skulle ta en termin att gå igenom på en gymnasieskola. Så syftet med dessa kurser är inte att eleverna ska kunna det som gåtts igenom efter kursens slut, utan eleverna måste själva laborera på egen hand många timmar efteråt.Detta kursupplägg fungerar bra för yrkesverksamma tekniker med tillgång till både hårdvara och mjukvara i sina arbeten och där möjligheten att vara borta från jobbet mer än en vecka inte är möjligt. Men frågan är om detta kursupplägg passar på en gymnasieskola.Hur ser då dessa kurser ut? Jo, de är upplagda så att föreläsningar och korta laborationer varvas. Föreläsningarna är inte speciella på något sätt. Läraren berättar och kompletterar med projekterat material. Det är snarare laborationerna som är speciella. De är utformade så att varje litet detaljsteg redovisas. Inget lämnas åt elevens förkunskap eller logiska slutsats. Eleven behöver bara kunna läsa för att kunna sätta upp en webbserver.Är då inte detta bra kan man fråga sig? Svaret är givetvis, det beror på vad man vill få ut av laborationen. Om syftet är att ge eleven en uppfattning om vad man kan göra med nätverksoperativsystemet eller om syftet är att sätta upp en webbserver (oavsett hur) når detta sätt sitt syfte. Men om syftet är att eleven verkligen ska lära sig hur man sätter upp en webbserver så att den kan upprepa samma uppgift en vecka eller en månad senare tror jag man går bet. Vad är då alternativet till detta sätt att göra laborationer? Ett sätt är att göra problemorienterade laborationer. En problemorienterad laborationsmanual är utformad så att bara de huvudsakliga uppgifterna som ska lösas är med. Ibland kan dock vissa tips vara med för att underlätta för eleverna. Eleven måste då själv reflektera över sitt handlande och återkoppla till den teori den fått på föreläsningen för att kunna klara uppgifterna.Jag menar att traditionella laborationsmanualer kopplar bort elevens logiska tänkande och engagemang och därmed minns de uppgifterna och lösningarna sämre. En problemorienterad laborationsmanual blir förmodligen jobbigare för eleven att utföra, men tvingar eleven att vara medveten om vad den gör.Sättet att göra laborationsmanualer till kurser om nätverksoperativsystem kan jämföras med hur naturvetenskapen, framför allt kemiundervisningen pratar kring frihetsgrader i sina laborationer. Man kan även sätta utförandet av laborationsmanualer i samband med hur problembaserat lärande ser på undervisningen och lärandet. / What impact has the design of a manual for laboratory experiments on how the students learn about computer networks? How does it affect what the students remember and how they manage to solve similar tasks?I have done a study of 31 students between 17 and 19 years old in a course about computer networks. Half of them received a manual for laboratory experiments, composed by a leading server operation system company. This manual represents how the traditional manual for laboratory experiments is designed. The other half received a manual, composed by me and represents how a more problem oriented manual is designed.After a few weeks I did a test to see how much the students remembered of what they had worked with during the lesson. They also had to do similar tasks so I could see how the manual for laboratory experiments affected their understanding of what they where doing. After the test the students had to estimate how much their manual had helped them with the test.The result of the study pointed in the direction that the manual for laboratory experiments which was designed to be problem oriented, forced the students to think about what they where doing. That was of course much tougher for the students, but the result was that they understood and remembered better what they were doing.

During the course of normal DNA replication, replication forks are constantly encountering "housekeeping" types of routine damage to the DNA template that may cause the forks to stall or collapse. One product of this fork collapse is the induction of the SOS response, a coordinated global response to help pause the growth and replication of a cell while DNA damage is addressed and repaired. In E. coli, this response is activated by the formation of ssDNA, to which the RecA protein binds and forms a nucleoprotein filament, which acts as the activator for autocleavage of the LexA transcriptional repressor, which normally represses expression of SOS genes. Damage responses are crucial to maintaining genomic integrity, and are therefore essential to all forms of life, and this type of regulatory system is highly conserved. However, cells have mechanisms for tightly regulating induction of these responses, and can often repair routine damage to their chromosomes without the need to induce SOS. This is chiefly evidenced by the observation that more than 20% of cells in a population have RecA filaments, but less than 1% are induced for SOS. How cells make this decision to induce SOS is the subject of this work. This dissertation describes three projects aimed at examining molecular mechanisms by which cells regulate RecA filaments, and therefore the decision to induce the SOS response. The first examines the disparity between the formation of RecA filaments, as evidenced by RecA-GFP foci, and the induction of SOS in the absence of damage, using a psulA-gfp reporter system. It is shown that there are three independent factors that repress SOS expression in undamaged E. coli cells. These are radA, the amount of recA in the cell, and in some circumstances recX. The first two limit SOS in wild type cells in the absence of external damage, while the third is an additional factor required in xthA mutants, likely due to the fact there are more RecA loading events in these mutants. These factors are thought to change the character and reduce the half-life and persistence of RecA filaments in the cell. The second project shows that suppression of SOS through the use of recA4162 and uvrD303 mutants is substrate and situation-specific. This specificity is demonstrated by the fact that, while both recA4162 and uvrD303 can suppress SOS in the SOS constitutive mutant recA730, recA4162 can only suppress SOS when the signal occurs at replication forks and not at any other place on the chromosome, while uvrD303 appears to suppress SOS with less specificity, and can suppress after UV (shown previously), at induced DSBs, and other places not directly at the replication fork. Here mutants of different replication factors are used that uncouple the replisome and induce SOS to a high degree. The third project determines the factors necessary for loading RecA filaments at the replication fork versus other locations on the chromosome when SOS is induced in the absence of damage, and helps elucidate further mechanisms for induction of SOS at these substrates. It is shown that the sbcB and recJ exonucleases assist in inappropriate RecA filament formation by substrate processing exclusively at replication forks, but not other substrates, likely through mechanisms that are reliant on the activities of the RecA loading factors RecBCD and RecFOR.

O-LiFE est un observatoire de l’environnement dédié à l’étude des ressources et de la biodiversité dans la zone critique à la vie, focalisé sur la méditerranée. C’est aussi une structure à l’interface entre la recherche fondamentale et les porteurs d’enjeux. Cette plateforme initiée en collaboration entre des équipes libanaises et françaises se focalise d’abord sur l’observation systémique du milieu naturel, autour des thématiques de l’eau, la biodiversité et la gestion de l’environnement. Le fondement de l’observatoire est la mise en oeuvre d’une approche transdisciplinaire du défi du changement global. Structurer, partager, pérenniser et valoriser les données environnementales constitue un objectif prioritaire pour permettre à une large communauté de converger vers une approche réellement systémique et transdisciplinaire des enjeux environnementaux en Méditerranée. La construction d’un système d’information permettant cette mise en relation complète des données est donc prioritaire. Cependant cette mise en oeuvre est rendu complexe par plusieurs défis à relever pour répondre aux utilisateurs finaux et producteurs de données qui ne partagent pas les mêmes besoins, et pour tenir compte de l’hétérogénéité naturelle des données.Dans cette thèse, nous détaillons par conséquent les réflexions et travaux menés pour la mise en place de l’architecture du SI de l’observatoire. Le travail a été initié par une enquête permettant de mieux connaître les sources de données existantes. Nous avons ensuite proposé d’utiliser les environnements de gestion de données d’observations basés sur des ontologies partagées et les recommandations des consortiums reconnus (OGC). Des extensions sont proposées pour permettre la prise en compte de points de vue distincts sur les données via des multi-mapping. Cette extension permet un découplage entre la vision initiale du producteur de données et les multiples utilisations possibles des données à l’aide de croisement avec d’autres sources de données et/ou d’autres points de vue.Nous avons enfin appliqué la méthodologie sur les données O-LiFE et avons pu extraire des croisements de données inter-bases (entre deux sources de données distinctes) et intra-bases (en juxtaposant des points de vue distincts sur une même source de données). Ce travail est une démonstration du rôle fondamental des outils du SI et des observatoires dans le rapprochement indispensable des communautés scientifiques autant que des porteurs d’enjeux pour la résolution des grands défis sociétaux environnementaux, notamment en Méditerranéen. / O-LiFE is an environmental observatory dedicated to the study of resources and biodiversity in the critical area of life, focused on the Mediterranean. It is also a structure at the interface between basic research and the holders of issues. This platform initiated in collaboration between Lebanese and French teams focuses first on systemic observation of the natural environment around the themes of water, biodiversity and environmental management. The foundation of the observatory is the implementation of a transdisciplinary approach to the challenge of global change.Organize, share, sustain and enhance environmental data is a priority objective to enable the wider community to converge towards a truly systemic and transdisciplinary approach to environmental issues in the Mediterranean. The construction of an information system allowing complete connection of data is therefore a priority. However, this implementation is complicated by a number of challenges to meet the end users and data producers expectations who do not share the same needs, and to take into account thenatural heterogeneity of data.In this PhD, we detail brainstorming and work needed for the development of the architecture of the information system of the observatory. The work was initiated by a survey to better understand theexisting sources of data. We then proposed to use observational data management environments based on shared ontologies and the recommendations of recognized consortia (OGC). Extensions are proposed to enable the inclusion of different perspectives on data through multi-mapping. This extension allows a decouplingbetween the original vision of the data producer and the many possible uses of the data with crossbreeding with other data sources and / or other views.We then applied the methodology on the O-LiFE data and were able to extract inter-data analysis (between two distinct data sources) and intra-bases analysis (by juxtaposing different points of view on the same data source). This work is a demonstration of the fundamental role of IS tools and observatories in the essential gathering of the scientific communities as much as stakeholders to resolve major environmental challenges facing society, particularly in Mediterranean.

La pression rencontrée par les organismes sur Terre varie de la pression atmosphérique à 110 MPa atteinte dans la fosse la plus profonde de l'océan. Même si Escherichia. coli n’est pas naturellement résistante à la pression, elle capable d'acquérir une résistance et même supporter un choc de pression de 2 GPa (~20 000 atm). L'une des réponses intéressantes d’E. coli à un choc sous létal de pression (100 MPa) est l'induction d'une réponse SOS dépendante de RecA due à des lésions double brins de l’ADN. La pression elle-même n'est pas capable de compromettre l'intégrité covalente de l'ADN. Des criblages ont permis d’isoler des souches d’E. coli résistantes à la pression qui révèlent qu'une endonucléase de restriction (ER) de type IV, Mrr, est le seul facteur responsable du clivage de l'ADN. Cette enzyme cible uniquement l'ADN méthylé et l’expression d’une MTase étrangère, M.HhaII, est également capable d'induire une réponse SOS dans des souches de E. coli en présence de Mrr. Ici, nous démontrons en utilisant des techniques de fluctuations d’intensité de fluorescence, in vivo et in vitro que Mrr est un présent sous la forme d’un tétramère dans les cellules non stressées. La pression est capable de dissocier Mrr en dimères actifs qui peuvent lier l'ADN et cliver à certains sites cryptiques. En revanche, la MTase HhaII favorise la forme dimeric de Mrr liée à l’ADN en raison de la méthylation de nombreux sites de haute affinité. Une analyse mutationnelle et un modèle d’homologie 3D de la protéine entière révèle la base structurelle probable du changement entre la forme tétramérique inactive à la forme dimérique active. Nous avons mis en pace un système permettant de faire de la microscopie sous pression (in vitro and in vivo) et nos résultats préliminaires ont confirmé notre modèle d’activation de Mrr. / The pressure encountered by organisms on Earth varies from the atmospheric pressure to 110 MPa as reached in the deepest trench of the ocean. Although Escherichia coli is not naturally resistant to high pressure, it is capable of acquiring pressure resistance and withstanding a pressure shock up to 2 GPa (~20,000 atm). When exposed to a sub-lethal pressure shock (100 MPa) E. coli induces a RecA-dependent SOS response due to DNA double strand breaks. Pressure itself is not capable of compromising the covalent integrity of the DNA. Instead, screens for pressure-resistance E. coli mutants have revealed that a Type IV restriction endonuclease, Mrr is the only factor responsible for DNA cleavage. This enzymes targets only methylated DNA and expression of a foreign methyltransferase, M.HhaII, is also capable of inducing an SOS response in strains harboring Mrr. Here, we demonstrate using fluorescence fluctuation techniques in vivo and in vitro that Mrr is present as a tetramer in unstressed cells and that pressure dissociates Mrr into active dimers that can bind DNA and cleave at some cryptic sites. In contrast, the M.HhaII MTase pulls the Mrr tetramer-dimer equilibrium to the dimer-bound DNA form probably due to the methylation of many high-affinity sites. Mutational analysis associated with a 3D homology model of the full-length protein reveals the probable structural basis for the switch from an inactive tetramer to an active dimer. We set up a system that allows microscopy experiments (in vitro and in vivo) under pressure and preliminary results have confirmed our model of Mrr activation.

Systems-of-Systems (SoS) encompass diverse and independent systems that must cooperate with each other for performing a combined action that is greater than their individual capabilities. In parallel, architecture descriptions, which are the main artifact expressing software architectures, play an important role in fostering interoperability among constituents by facilitating the communication among stakeholders and supporting the inspection and analysis of the SoS from an early stage of its life cycle. The main problem addressed in this thesis is the lack of adequate architectural descriptions for SoS that are often built without an adequate care to their software architecture. Since constituent systems are, in general, not known at design-time due to the evolving nature of SoS, the architecture description must specify at design-time which coalitions among constituent systems are feasible at run-time. Moreover, as many SoS are being developed for safety-critical domains, additional measures must be placed to ensure the correctness and completeness of architecture descriptions. To address this problem, this doctoral project employs SoSADL, a formal language tailored for the description of SoS that enables one to express software architectures as dynamic associations between independent constituent systems whose interactions are mediated for accomplishing a combined action. To synthesize concrete architectures that adhere to one such description, this thesis develops a formal method, named Ark, that systematizes the steps for producing such artifacts. The method creates an intermediate formal model, named TASoS, which expresses the SoS architecture in terms of a constraint satisfaction problem that can be automatically analyzed for an initial set of properties. The feedback obtained in this analysis can be used for subsequent refinements or revisions of the architecture description. A software tool named SoSy was also developed to support the Ark method as it automates the generation of intermediate models and concrete architectures, thus concealing the use of constraint solvers during SoS design and development. The method and its accompanying tool were applied to model a SoS for urban river monitoring in which the feasibility of candidate abstract architectures is investigated. By formalizing and automating the required steps for SoS architectural synthesis, Ark contributes for adopting formal methods in the design of SoS architectures, which is a necessary step for obtaining higher reliability levels. / Sistemas-de-sistemas (SoS) englobam sistemas diversos e independentes que cooperam entre si para executar uma ação combinada que supera suas competências individuais. Em paralelo, descrições arquiteturais são artefatos que expressam arquiteturas de software, desempenhando no contexto de SoS um importante papel na promoção da interoperabilidade entre constituintes ao facilitar a comunicação entre interessados e apoiar atividades de inspeção e análise desde o início de seu ciclo de vida. O principal problema abordado nessa tese consiste na falta de descrições arquiteturais adequadas para SoS que estão sendo desenvolvidos sem um devido cuidado à sua arquitetura de software. Uma vez que os sistemas constituintes não são necessariamente conhecidos em tempo de projeto devido à natureza evolucionária dos SoS, a descrição arquitetural precisa definir em tempo de projeto quais coalisões entre sistemas constituintes são possíveis em tempo de execução. Como muitos desses sistemas são desenvolvidos para o domínio crítico de segurança, medidas adicionais precisam ser adotadas para garantir a correção e completude da descrição arquitetural. Visando tratar esse problema, esse projeto de doutorado emprega SosADL, uma linguagem formal criada especialmente para o domínio de SoS que permite expressar arquiteturas de software como associações dinâmicas entre sistemas independentes em que as interações devem ser mediadas para desempenhar uma ação conjunta. Em particular, é proposto um novo método formal, denominado Ark, para sistematizar os passos necessários na síntese de arquiteturas concretas aderentes a essa descrição. Para isso, o método cria um modelo formal intermediário, denominado TASoS, que expressa a arquitetura do SoS em termos de um problema de satisfatibilidade de restrições, possibilitando desse modo a verificação automática de um conjunto inicial de propriedades. O resultado obtido por essa análise pode ser utilizado em refinamentos e revisões subsequentes da descrição arquitetural. Uma ferramenta de apoio denominada SoSy também foi desenvolvida para automatizar a geração de modelos intermediários e arquiteturas concretas, ocultando o uso de solucionadores de restrições no projeto e desenvolvimento de SoS. O método e sua ferramenta foram aplicados em um modelo de SoS para monitoramento de rios em áreas urbanas em que a viabilidade de arquiteturas abstratas foi investigada. Ao formalizar e automatizar os passos necessários para a síntese arquitetural de SoS, é possível adotar métodos formais no projeto arquitetural de SoS, que são necessários para alcançar níveis maiores de confiabilidade.

Les concentrations sous-inhibitrices (sub-CMI) de antibiotiques jouent un rôle important dans la sélection et le développement des résistances. Contrairement à Escherichia coli, Vibrio cholerae induit la réponse SOS en présence de sub-CMI d'aminosides. SOS est également impliquée dans la plasticité du génome et dans l'acquisition de la résistance aux antibiotiques. Afin de sélectionner des mutants de V. cholerae qui n'induisent pas SOS en présence de sub-CMI d'aminosides, nous avons développé un crible génétique pour l'isolement de mutants dans lesquels l'induction de la réponse SOS est perdue. L'un de ces mutants est inactivé pour le gène radD, qui code pour une hélicase ADN/ARN putative. RadD est impliquée dans la résolution de cassures d'ADN double brin (DSB) provoquées par des sub-CMI de tobramycine. Nous avons montré que les R-loops sont à l'origine des DSB formés en absence de radD en tobramycine. Nous suggérons que les lésions de l'ADN formées lors du traitement par aminoglycosides soient réparées par la formation d'intermédiaires ssDNA induisant SOS. L’ARNPol bloquée sur ces lésions peut faciliter la formation de R-loops qui, si elles ne sont pas réparées, peuvent entraîner la formation de DSB et l'instabilité du génome. RadD pourrait jouer un rôle dans la résolution des R-loops. Ces résultats ont mis en évidence le fait que les sub-CMI de tobramycine conduisent à DSB, dues en partie aux R-loops. La tobramycine est un aminoside qui cible le ribosome. La formation de DSB par un tel antibiotique peut être surprenante car la formation de lésions de l'ADN par un antibiotique qui cible la traduction n'est pas attendue. Afin de comprendre les voies impliquées dans la réponse à de sub-CMI de tobramycine, nous avons adopté une approche Tn-seq à haut débit pour déterminer quels gènes sont importants pour maintenir l'intégrité de la cellule en présence d'antibiotiques à faibles doses. / Sub-inhibitory concentrations (sub-MIC) of antibiotics play an important role in selection and development of resistances. Unlike Escherichia coli, Vibrio cholerae induces its SOS response in presence of sub-MIC aminoglycosides. SOS is also involved in genome plasticity and in the acquisition of resistance to antibiotics. In order to select for V. cholerae mutants that do not induce low aminoglycoside-mediated SOS induction, we developed a genetic screen for the isolation of mutants in which induction of the SOS response by sub-MICs of aminoglycosides is lost. One of these mutants is inactivated for the radD gene, which encodes a putative DNA/RNA helicase. RadD is involved in the resolution of double strand DNA breaks caused by treatment with sub-MIC of tobramycine. We demonstrate that R-loops are at the origin of DSBs formed in the absence of radD in tobramycine.We propose that DNA lesions formed upon aminoglycoside treatment are repaired through the formation of ssDNA intermediates, inducing SOS. RNAP could stalls on these lesions and forms R-loops, that, if not repaired, can lead to the formation of DSB and genome instability. RadD could play a role in the resolution of R-loops. These results highlighted the fact that sub-MIC of tobramycine leads to DNA double strand breaks, at least partly through R-loop formation. Tobramycin is an aminoglycoside that targets the ribosome. The formation of DSBs by such an antibiotic can be surprising as DNA damage formation by an antibiotic that targets translation is not expected. In order to understand the pathways involved in the response to low doses of tobramycin we adopted a high throughput Tn-seq approach to determine which genes are important in maintaining the integrity of the cell in the presence of antibiotics at low doses.

Bakalauro darbas „SOS! GMO!” atspindi šių dienų aktualijas, paliesdamas visuomenei svarbų klausimą apie genetiškai modifikuotų organizmų poveikį augmenijai ir gyvūnijai. Pirmame skyriuje analizuojama genetiškai modifikuotų organizmų plėtra pasaulyje, nagrinėjami teigiami ir neigiami GMO aspektai, pristatoma mokslininkų nuomonė, apie vartojamų GM produktų pavojų ne tik vabzdžių, bet ir žinduolių sveikatai. Remiantis atliktų tyrimų duomenimis su gyvūnais, numatoma, kad ateities kartos gali išsigimti ir tapti nevaisingomis. Antrame darbo skyriuje nagrinėjami įvairių menininkų sukurti darbai, kuriuose refleksuojamos ekosistemos problemos, pateikiami vizualūs skulptūros, keramikos, grafikos, baldų dizaino, fotomontažų, žemės meno, drabužių dizaino pavyzdžiai vaizdžiai parodantys autorių pozicija šiuo klausimu. Trečiajame skyriuje pagrindžiama drabužių kolekcijos idėja. Pateikiami vizualūs meniniai ieškojimai, technologiniai mėginiai, brėžiniai. Taip pat įvykdytos kolekcijos fotosesijos ir planšeto nuotraukos. Ketvirtame skyriuje aptariamos sukurtos darbužių kolekcijos realizavimo galimybės , taip pat pateikiama kolekcijos sąmata. Drabužių neplanuojama parduoti greitu metu, nes norima ją papildyti ir dalyvauti madų renginiuose, taip garsinti dizainerės vardą. Įgyvendintų modelių savikaina yra 866,79 Lt, pardavimo kaina – 948,41 Lt, planuojamas pelnas 82 Lt. Išanalizuota informacija suteikė galimybę sukurti drabužių kolekciją „SOS! GMO!“, kurioje interpretuojamas genetiškai... [toliau žr. visą tekstą] / Bachelor work “SOS! GMO!” reflects nowadays realities addressing the public about the important issue of genetically modified organisms on the flora and fauna. The development of genetically modified organisms in the world is analized in the first section and also the positive and negative aspects of GMO`s are examined. Moreover, scientists opinion on the risk of GM products not only for insects but for mammalian health is represented. According to studies conducted in animals, it is envisaged that future generations can degrade and become infertile. Created works of various artists are dealt in the second section where ecosystem problems are reflexed. The visual sculptures, ceramics, graphics, furniture design, montages, land art, clothing design examples illustrating the authors` position on this issue are introduced. The third section justified the idea of clothing collection. The visual artistic designs, technological samples, drawings are given. Furthermore, the collection of photo sessions and flatbed photo are fulfilled. The fourth chapter deals with outlets of the created clothing collection and also an estimate of the collection provided. The clothes are not planed to sell in a short time due to the fact that it is intended to accession the collection and participate in fashion events. It helps to glorify the name of the designer. The cost of implemental models is 866,79 Lt, sale price - 948,41 Lt, expected profit - 82 Lt. The analysis of information helped to... [to full text]

Systems-of-Systems (SoS) encompass diverse and independent systems that must cooperate with each other for performing a combined action that is greater than their individual capabilities. In parallel, architecture descriptions, which are the main artifact expressing software architectures, play an important role in fostering interoperability among constituents by facilitating the communication among stakeholders and supporting the inspection and analysis of the SoS from an early stage of its life cycle. The main problem addressed in this thesis is the lack of adequate architectural descriptions for SoS that are often built without an adequate care to their software architecture. Since constituent systems are, in general, not known at design-time due to the evolving nature of SoS, the architecture description must specify at design-time which coalitions among constituent systems are feasible at run-time. Moreover, as many SoS are being developed for safety-critical domains, additional measures must be placed to ensure the correctness and completeness of architecture descriptions. To address this problem, this doctoral project employs SoSADL, a formal language tailored for the description of SoS that enables one to express software architectures as dynamic associations between independent constituent systems whose interactions are mediated for accomplishing a combined action. To synthesize concrete architectures that adhere to one such description, this thesis develops a formal method, named Ark, that systematizes the steps for producing such artifacts. The method creates an intermediate formal model, named TASoS, which expresses the SoS architecture in terms of a constraint satisfaction problem that can be automatically analyzed for an initial set of properties. The feedback obtained in this analysis can be used for subsequent refinements or revisions of the architecture description. A software tool named SoSy was also developed to support the Ark method as it automates the generation of intermediate models and concrete architectures, thus concealing the use of constraint solvers during SoS design and development. The method and its accompanying tool were applied to model a SoS for urban river monitoring in which the feasibility of candidate abstract architectures is investigated. By formalizing and automating the required steps for SoS architectural synthesis, Ark contributes for adopting formal methods in the design of SoS architectures, which is a necessary step for obtaining higher reliability levels. / Sistemas-de-sistemas (SoS) englobam sistemas diversos e independentes que cooperam entre si para executar uma ação combinada que supera suas competências individuais. Em paralelo, descrições arquiteturais são artefatos que expressam arquiteturas de software, desempenhando no contexto de SoS um importante papel na promoção da interoperabilidade entre constituintes ao facilitar a comunicação entre interessados e apoiar atividades de inspeção e análise desde o início de seu ciclo de vida. O principal problema abordado nessa tese consiste na falta de descrições arquiteturais adequadas para SoS que estão sendo desenvolvidos sem um devido cuidado à sua arquitetura de software. Uma vez que os sistemas constituintes não são necessariamente conhecidos em tempo de projeto devido à natureza evolucionária dos SoS, a descrição arquitetural precisa definir em tempo de projeto quais coalisões entre sistemas constituintes são possíveis em tempo de execução. Como muitos desses sistemas são desenvolvidos para o domínio crítico de segurança, medidas adicionais precisam ser adotadas para garantir a correção e completude da descrição arquitetural. Visando tratar esse problema, esse projeto de doutorado emprega SosADL, uma linguagem formal criada especialmente para o domínio de SoS que permite expressar arquiteturas de software como associações dinâmicas entre sistemas independentes em que as interações devem ser mediadas para desempenhar uma ação conjunta. Em particular, é proposto um novo método formal, denominado Ark, para sistematizar os passos necessários na síntese de arquiteturas concretas aderentes a essa descrição. Para isso, o método cria um modelo formal intermediário, denominado TASoS, que expressa a arquitetura do SoS em termos de um problema de satisfatibilidade de restrições, possibilitando desse modo a verificação automática de um conjunto inicial de propriedades. O resultado obtido por essa análise pode ser utilizado em refinamentos e revisões subsequentes da descrição arquitetural. Uma ferramenta de apoio denominada SoSy também foi desenvolvida para automatizar a geração de modelos intermediários e arquiteturas concretas, ocultando o uso de solucionadores de restrições no projeto e desenvolvimento de SoS. O método e sua ferramenta foram aplicados em um modelo de SoS para monitoramento de rios em áreas urbanas em que a viabilidade de arquiteturas abstratas foi investigada. Ao formalizar e automatizar os passos necessários para a síntese arquitetural de SoS, é possível adotar métodos formais no projeto arquitetural de SoS, que são necessários para alcançar níveis maiores de confiabilidade.

Les travaux présentés dans cette thèse ont porté sur la specificité des réponses cellulaires de l’halophyte obligatoire Cakile maritima au choc salin et la régulation des événements précoces impliqués dans la mort cellulaire programmée et la survie en condition de salinité. Dans une première étape, nous avons montré que cette plante est aussi tolérante aux chocs salins répétés qu’au stress salin progressif. Cependant, on a observé de zones de mort cellulaires sur les feuilles âgées soumises à un choc salin sévère (400 mM NaCl). Pour mieux cerner la cascade d’événements impliqués dans ce processus de mort cellulaire, nous avons poursuivi nos expériences sur des suspensions cellulaires de C. maritima, dont nous avons-nous même optimisé les conditions d’obtention, et des suspensions cellulaires d’Arabidopsis thaliana (glycophyte modèle). Chez les deux espèces, nous avons observé une mort cellulaire programmée qui dépend de la durée et l’intensité du traitement salin appliqué, et qui met en jeu les mêmes événements cellulaires notamment la dépolarisation de la membrane plasmique due à l’entrée de Na+ par les NSCCs, un dysfonctionnement mitochondrial, une production d’anions superoxydes et une activation de protéines de type caspase. La tolérance de C. maritima au stress salin serait potentiellement due à une forte accumulation d’ascorbate qui permettrait à cette halophyte de mieux réduire les dommages générés par le stress oxydatif. C. maritima s’est aussi distinguée par une meilleure capacité de contrôler l’accumulation cytoplasmique de Na+, conduisant à la survie de ses cellules en condition de salinité. Cette étude sur la mort cellulaire induite par le NaCl chez les cellules en culture de C. maritima nous a aussi permis de mettre en évidence deux types de comportement dans cette population de cellules en culture : l’un lié à une dépolarisation soutenue en réponse au NaCl conduisant probablement à la mort de ces cellules, l’autre lié à une dépolarisation transitoire indiquant que l’influx de Na+ au travers des NSCC était régulé permettant probablement aux cellules présentant ce comportement de survivre en évitant l'accumulation excessive de Na+ dans le cytosol. Dans la dernière partie de ce travail, nous avons mis en évidence la capacité de C. maritima d’exclure Na+ via le système SOS. Ce résultat suggère l’existence d’une deuxième voie de signalisation induite parallèlement à celle conduisant à la mort cellulaire. Cette voie, impliquant une production rapide d’oxygène singulet, pourrait permettre un influx de Ca2+ dans le cytoplasme activant la protéine SOS3 et en cascade SOS2 et SOS1 et les H+-ATPases de la membrane plasmique permettant un efflux du Na+ via SOS1 hors des cellules. / AbstractThis work aimed at understanding the specificity of cellular responses of the obligate halophyte Cakile maritima to salt shock and regulation of early events involved in programmed cell death and survival under salinity conditions. In a first step, we have shown that this plant is tolerant upon both repetitive salt shocks and gradual salt application. However, we have observed a cell death zones on older leaves subjected to a severe shock saline (400 mM NaCl). To better understand the cascade of events involved in the cell death process, we continued our experiments on suspension culture of C. maritima, which we have optimized ourselves the conditions for establishment and suspension culture of Arabidopsis thaliana (glycophyte model). In both species, salinity induced programmed cell death that depends on the duration and the intensity of the applied salt treatment. Also, the same cellular events, including depolarization of the plasma membrane due to the Na+ influx by NSCCs, mitochondrial dysfunction, production of superoxide anions and activation of caspase-like proteins, occurs early in response to salt stress. C. maritima tolerance to salt stress is potentially due to a strong accumulation of ascorbate that would allow this halophyte to better reduce damage generated by oxidative stress. C. maritima is also distinguished by a better ability to control the cytoplasmic accumulation of Na+, leading to the survival of its cells under salinity conditions. This study on cell death induced by NaCl in cell culture of C. maritima also allowed us to identify two types of behavior in this population of cells in culture: one related to a sustained depolarization in response to NaCl probably leading to death of these cells, the other linked to a transient depolarization indicating that the Na+ influx through the NSCC was probably regulated allowing cells exhibiting this behavior to survive by avoiding excessive accumulation of Na+ in the cytosol. In the last part of this work, we have demonstrated the ability of C. maritima to exclude Na+ via the SOS system. This result suggests the existence of a second signaling pathway induced in parallel to that leading to cell death. This pathway, involving a rapid production of singlet oxygen, could allow a Ca2+ influx in the cytoplasm that acts as an elicitor for activation of SOS3 protein and SOS2-SOS1 cascade and H+- ATPases of the plasma membrane allowing Na+ efflux via SOS1 out of cells.