Presented master thesis is dedicated to creation of DEECo component model supported on Android platform. Enabling distributed system of inter-connected devices to run DEECo framework. For this purpose jDEECo implementation of DEECo component model is ported to Android platform and synchronization solution creating common state is done on top of JGroups toolkit. Possible solutions are presented and implementation of created solution is described. At last demo application showing usage of created framework was developed and evaluated.

Lactobacillus casei es una bacteria del ácido láctico de interés aplicado por su uso como cultivo iniciador en la industria alimentaria y por el carácter probiótico de algunas cepas. Como probiótico, L. casei debe sobrevivir a las condiciones de producción industrial y a su paso por el tracto gastrointestinal manteniendo sus propiedades. Para ello, L. casei posee rutas de reconocimiento de señales ambientales específicas y convierten esta información en una respuesta fisiológica adecuada. Un mecanismo comúnmente encontrado en bacterias para la transducción de señal son los sistemas de dos componentes (Two Components Systems, TCS). Los TCS están formados por una proteína sensora con actividad histidina quinasa (HK) y un regulador de respuesta (RR). La detección de un estímulo específico por la proteína sensora induce su autofosforilación y la transferencia del fosfato al regulador de respuesta, produciéndose la activación del mismo. Los sistemas de dos componentes median la respuesta adaptativa a una amplia gama de estímulos ambientales en bacterias. En el laboratorio de Bacterias Lácticas del Instituto de Agroquímica y Tecnología de Alimentos se ha iniciado el estudio de los TCS codificados por L. casei BL23 dentro del cual se incluye el presente proyecto de tesis doctoral. / Revilla Guarinos, A. (2014). Characterization of Two Component Systems of Lactobacillus casei BL23 and their involvement in stress response [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/43589

Streptococci resident in the oral cavity have been linked to infective endocarditis (IE). While viridans streptococci are commonly studied and associated with IE, less research has been focused on Streptococcus pneumoniae. Two-component systems (TCSs), consisting of a histidine kinase (HK) protein and response regulator (RR) protein, are bacterial signaling systems that may mediate S. pneumoniae TIGR4 strain virulence in IE. To test this hypothesis, TCS RR mutants of TIGR4 were examined in vivo through use of rabbit models. There were 14 RR proteins identified and 13 RR mutants synthesized because SP_1227 was found to be essential. The requirement of the 13 RRs for S. pneumoniae growth in IE models was assessed by quantifying mutants after overnight inoculation in IE infected rabbits through use of real time PCR (qPCR), colony enumeration on antibiotic selection plates, and competitive index assays. Real time PCR pinpointed several candidate virulence factors. Candidate RR SP_0798 was selected to be further examined. In the in vivo model, mutant SP_0798 grew significantly less than our control mutant SP_1678, which encodes a hypothetical protein and grew at a comparable rate to wild-type TIGR4 strains. Literature and databases identified SP_0798 as the ciaR gene, which has roles in regulating many diverse cellular functions. Our data suggests that RR SP_0798 is a virulence factor of S. pneumoniae TIGR4 strain in IE. This research may place more emphasis on virulence factors and lead to novel methods to combat pneumococcal endocarditis.

Two-component systems (TCS) are the predominant signal transduction pathways in prokaryotes, being present also in eukaryotic organisms, such as algae, fungi and yeast, and higher plants. TCSs play an important role in environmental signal perception and response, essentially implementing adaptation to the surrounding environment. Histidine Kinase 2 (Hik2) in cyanobacteria is a typical sensor histidine kinase, one component of a TCS, and has been identified to be a homologue protein of Arabidopsis Chloroplast Sensor Kinase (CSK). Previous research has elucidated Hik2 to regulate photosynthetic gene transcription with two response regulators, Rre1 and RppA via phosphorylation. A typical histidine kinase contains a variable sensor domain and a conserved kinase domain. It usually functions as a homodimer. This thesis describes the structural characterisation of Hik2, probing particularly its discovered oligomeric states. Results obtained from size exclusion chromatography, native-PAGE, chemical cross-linking analyses and mass spectrometry, amongst others, have shown a variety of Hik2 structural populations exist, further validated by negative stain transmission electron microscopy coupled to single particle analysis. Hik2 protein exists predominantly as a hexamer in low salt conditions, and adding NaCl dissociates hexamers into tetramers, critical for the autophosphorylation activity of Hik2. Thus, a model is proposed for the constitution change of Hik2 oligomers when salt concentration differs. In addition, the sensor domain is typically responsible for detecting environmental input, however, it is not yet clear how Hik2 and CSK sense signals. In this thesis, the structures of Hik2 and CSK sensor domains were analysed and discussed, to aid our understanding of their mechanism of signal perception and transduction.

The condition monitoring of multi-component systems utilizes multiple sensors to capture the functional condition of the systems and allows the sensor information to be used to reason about the health information of the systems or components. Chapter 3 considers the situation when sensor signals capture unknown mixtures of component signals and proposes a two-stage vibration-based methodology to identify component degradation signals from mixed sensor signals in order to predict component-level residual lives. Specifically, we are interested in modeling the degradation of systems that consist of two or more identical components operating under similar conditions. Chapter 4 focuses on the interactive relationship between tool wear (component degradation) and product quality degradation (sensor information) that widely exists in multistage manufacturing processes and proposes a high-dimensional stochastic differential equation model to capture the interaction relationship. Then, real-time quality measurements are incorporated to online predict the residual life of the system. Chapter 5 develops a strategy of dynamic workload adjustment for parallel multi-component systems in order to control the degradation processes and failure times of individual components, for the purpose of preventing the overlap of component failures. This chapter opens a new research direction that focuses on the active control of degradation rather than only the modeling part.

Doctor of Philosophy / Department of Computing and Information Sciences / John M. Hatcliff / Software architectures—abstract interrelation models which decompose complex artifacts into modular functional units and specify the connections and relationships among them—have become an important factor in the development and maintenance of large scale, heterogeneous, information and computation systems. In system development, software architecture design has become a main starting point, and throughout the life-cycle of a system, conformance to the architecture is important to guarantee a system's integrity and consistency. For an effective use of software architectures in initial development and ongoing maintenance, the interrelation models themselves have to be clear, consistent, well structured, and—in case substantial functionality has to be added, reduced, or changed at any stage of the life cycle—flexible and manipulable. Further, enforcing the conformance of a software artifact to its architecture is a non-trivial task. Implementation units need to be identifiable and their association to the abstract constructs of the architecture has to be maintained. Finally, since software architectures can be employed at many different levels of abstraction, with some architectures describing systems that span over multiple different computing platforms, associations have to be flexible and abstractions have to be general enough to capture all parts and precise enough to be useful. An efficient and widely used way to employ software architecture in practice are middleware-based component architectures. System development within this methodology relies on the presence of a service layer called middleware which usually resides between operating system (possibly spanning over multiple operating systems on various platforms) and the application described by the architecture. The uniform set of logistic services provided by a middleware allows that communication and context requirements of the functional units, called components, can be expressed in terms of those services and therefore more shortly and concisely than without such a layer. Also, component development in the middleware context can focus on high-level functionality since the low-level logistics is provided by the middleware. While type systems have proved effective for enforcing structural constraints in programs and data structures, most architectural modeling frameworks include only weak notions of typing or rely on first-order logic constraint languages instead. Nevertheless, a consequent, adherent, use of typing can seamlessly enforce a wide range of constraints crucial for the structural integrity of architectures and the computation systems specified by them without the steep learning curve associated with first-order logic. Also, type systems scale better than first-order logic both in use and understandability/legibility as well as in computational complexity. This thesis describes component-oriented architecture modeling with CADENA and introduces the CADENA Architecture Language with Meta-modeling (CALM). CALM uses multi-level type systems to specify complex interaction models and enforce a variety of structural properties and consistency constraints relevant for the development of large-scale component-based systems. Further, CALM generalizes the notion of middleware-based architectures and uniformly captures and maintains complex interrelated architectures integrated on multiple, differing, middleware platforms. CADENA is a robust and extensible tool based on the concepts and notions of CALM that has been used to specify a number of industrial-strength component models and applied in multiple industrial research projects on model-driven development and software product lines.

No description available.

This dissertation will investigate how Product Performance Contracts are organized in Multi Component Systems contexts that proliferate contemporary OEM industries. The last two decades have seen a big change in both practice as well as the product engineering technologies that form the ecosystem within which suppliers and buyers negotiate the scale and scope of their transaction contracts. While we have seen the focus of industrial procurement move from specifications based contracts to performance based contracts, we are also witnessing a burgeoning technological capability that allows remote monitoring of product performance. These capabilities are part of the interconnectivity driving the much-touted Internet of Things (IoT) technology and at the heart of the Industrial Big Data ecosystem. The dissertation will attempt to explain three major phenomena in the industrial buyer and seller relationship in the context of Multi Component System Industries. First, we uncover the factors that explain the choice of product performance contract specificity between the OEM and suppliers. We first set up an analytical model to explain the notion of an optimal contract specificity level and predict and further empirically test the role of different factors in the choice of contract specificity. We find that while the technology uncertainty decreases the level of optimal contract specificity, OEM’s transaction specific investment, unconstrained mixing-and-matching of branded component, and extent of product monitoring technology increases the level of optimal contract specificity. Second, we provide empirical evidence that any deviation from optimal contract specificity erodes value in the form of an increase in total transaction cost. In our transaction cost efficiency model, we also illustrate with a precise granularity that under-specified contracts lead to more ex-post dispute costs, and over-specified contracts lead to more ex-post contract monitoring cost and ex-ante contract writing cost. Third, we investigate how contracts, investments in strategic capabilities such as monitoring technology, the overall firm strategy, and transaction costs determine the firm performance. We find that not every transaction cost is a dead weight loss in terms of product performance. Most notably we find that ex-post dispute costs are associated with higher product performance when there is a major incident such as component failure between the OEM and the supplier. Methodologically, this dissertation proposes to use a combination of field work, mathematical modeling, conceptual theory building, and empirical analysis of primary data about firm practices. / Thesis / Doctor of Philosophy (PhD)

The immediate goal of this thesis was the analysis of a three-component system whose major component was water. This analysis was to be the result of a procedure which could be readily extended to more complex systems.

Bacillus cereus sensu stricto (ss) est un pathogène alimentaire majeur représentant la 2e cause de toxiinfectionalimentaire en France en 2012. Cette espèce fait partie du groupe Bacillus cereus sensu lato (sl)constitué d’espèces ubiquitaires génétiquement très proches et incluant d’autres pathogènes comme B.anthracis, B. thuringensis et B. cytotoxicus. Les souches de B. cereus sl sont d’autre part réparties en septgroupes phylogénétiques présentant des gammes de température de croissance variées et caractérisés partrois thermotypes principaux: thermotolérants, mésophiles, psychrotolérants. L’adaptation au froid dessouches B. cereus ss est un mécanisme clé car il conditionne sa capacité à se développer dans les alimentsréfrigéré pour atteindre des doses qui peuvent être dangereuse pour les consommateurs. Le but de cetteétude a été d’étudier les mécanismes moléculaires impliqués dans l’adaptation au froid de la diversité desouches représentant B. cereus sl.Nous avons mis en évidence que les gènes codant pour le système à deux composants CasK/R sontsurexprimés à basse température. CasK/R s’est révélé être un système générique d’adaptation de B. cereussl au froid, car son rôle a été mis en évidence lors de l’étude de quatre souches de thermotypes différents etleurs mutants isogéniques ΔcasK/R respectifs. Une étude transcriptomique réalisée sur une souche ATCC14579 et son mutant ΔcasK/R a révélé que seize des gènes différentiellement exprimés en début de phaseexponentielle et en phase stationnaire, à basse température, codent pour des protéines impliquées dans lemétabolisme des acides gras. Nous avons mis en évidence le rôle de CasK /R dans la modification de lacomposition en acides gras membranaires via une augmentation de la proportion en acides gras insaturéslors de la croissance de B. cereus au froid. Par ailleurs, le gène codant pour la désaturase DesA,principalement responsable des insaturations des acides gras à basse température est régulée positivementpar CasK/R au froid.Nous avons également démontré que les gènes casK/R sont organisés en opéron avec un gène codant pourun régulateur RpiR-like. De manière originale, cet opéron est négativement régulé par CasK/R à bassetempérature en phase stationnaire. Le promoteur individuel du rpiR est réprimé à basse température maisaussi à température optimale de croissance, ce qui suggère un rôle de CasK/R, même à températureoptimale / Bacillus cereus sensu stricto (ss) is a major foodborne pathogen representing the second cause of foodpoisoning in France in 2012. This species belongs to Bacillus cereus sensu lato (sl) consisting of ubiquitousspecies genetically close-related and including other pathogens such as B. anthracis, B. thuringiensis and B.cytotoxicus. The strains of B. cereus sl are divided into seven phylogenetic groups with various growthtemperature ranges and characterized by three main thermotypes: thermotolerant, mesophilic,psychrotolerant. The B. cereus ss cold adaptation is a key mechanism because it determines B. cereusability to grow in refrigerated foods and achieve doses that can be dangerous to consumers. The aim of thisstudy was to study the molecular mechanisms involved in the cold adaptation of strains representing B.cereus sl diversity.We demonstrated that the genes encoding the two component system CasK/R are overexpressed at lowtemperature. CasK/R was found to be a generic mechanism for B. cereus sl cold adaptation as its role washighlighted in the study of four strains with different thermotypes and their respective isogenic mutantsΔcasK/R. A transcriptomic study on a B. cereus ATCC 14579 strain and its ΔcasK/R mutant strain revealedthat sixteen of the genes differentially expressed in both early log phase and stationary phase at lowtemperature encode proteins involved in the fatty acids metabolism. We showed the role of CasK/R in themodification of the membrane fatty acid composition via an increase of the proportion of unsaturated fattyacids during growth of B. cereus at low temperature. Furthermore, the gene encoding the desaturase DesA,mainly responsible of the fatty acids unsaturation at a low temperature is upregulated by CasK/R at lowtemperature.We also demonstrated that casK/R genes were organized in operon with a gene encoding a RpiR-likeregulator. Interstingly,, this operon is negatively regulated by CasK/R at low temperature in the stationaryphase. The individual rpiR promoter is repressed by CasK/R at low temperature but also optimal growthtemperature, suggesting also a role for CasK/R at optimal temperature