RinA controls phage-mediated packaging and transfer of virulence genes in gram-positive bacteria

Phage-mediated transfer of microbial genetic elements plays a crucial role in bacterial life style and evolution. In this study, we identify the RinA family of phage-encoded proteins as activators required for transcription of the late operon in a large group of temperate staphylococcal phages. RinA binds to a tightly regulated promoter region, situated upstream of the terS gene, that controls expression of the morphogenetic and lysis modules of the phage, activating their transcription. As expected, rinA deletion eliminated formation of functional phage particles and significantly decreased the transfer of phage and pathogenicity island encoded virulence factors. A genetic analysis of the late promoter region showed that a fragment of 272 bp contains both the promoter and the region necessary for activation by RinA. In addition, we demonstrated that RinA is the only phage-encoded protein required for the activation of this promoter region. This region was shown to be divergent among different phages. Consequently, phages with divergent promoter regions carried allelic variants of the RinA protein, which specifically recognize its own promoter sequence. Finally, most Gram-postive bacteria carry bacteriophages encoding RinA homologue proteins. Characterization of several of these proteins demonstrated that control by RinA of the phage-mediated packaging and transfer of virulence factor is a conserved mechanism regulating horizontal gene transfer.

Gröbner basis techniques for certain problems in coding and systems theory

There is much common ground between the areas of coding theory and systems theory. Fitzpatrick has shown that a Göbner basis approach leads to efficient algorithms in the decoding of Reed-Solomon codes and in scalar interpolation and partial realization. This thesis simultaneously generalizes and simplifies that approach and presents applications to discrete-time modeling, multivariable interpolation and list decoding. Gröbner basis theory has come into its own in the context of software and algorithm development. By generalizing the concept of polynomial degree, term orders are provided for multivariable polynomial rings and free modules over polynomial rings. The orders are not, in general, unique and this adds, in no small way, to the power and flexibility of the technique. As well as being generating sets for ideals or modules, Gröbner bases always contain a element which is minimal with respect tot the corresponding term order. Central to this thesis is a general algorithm, valid for any term order, that produces a Gröbner basis for the solution module (or ideal) of elements satisfying a sequence of generalized congruences. These congruences, based on shifts and homomorphisms, are applicable to a wide variety of problems, including key equations and interpolations. At the core of the algorithm is an incremental step. Iterating this step lends a recursive/iterative character to the algorithm. As a consequence, not all of the input to the algorithm need be available from the start and different "paths" can be taken to reach the final solution. The existence of a suitable chain of modules satisfying the criteria of the incremental step is a prerequisite for applying the algorithm.

Reliability of power electronic modules

The electric car, the all electric aircraft and requirements for renewable energy are examples of potential technologies needed to address the world problem of global warming/carbon emission etc. Power electronics and packaged modules are fundamental for the underpinning of these technologies and with the diverse requirements for electrical configurations and the range of environmental conditions, time to market is paramount for module manufacturers and systems designers alike. This paper details some of the results from a major UK project into the reliability of power electronic modules using physics of failure techniques. This paper presents a design methodology together with results that demonstrate enhanced product design with improved reliability, performance and value within acceptable time scales

Autoclave Cure Simulation of Composite Structures Applying Implicit and Explicit FE

Simulation of the autoclave manufacturing technique of composites can yield a preliminary estimation of induced residual thermal stresses and deformations that affect component fatigue life, and required tolerances for assembly. In this paper, an approach is proposed to simulate the autoclave manufacturing technique for unidirectional composites. The proposed approach consists of three modules. The first module is a Thermo-chemical model to estimate the temperature and the degree of cure distributions in the composite part during the cure cycle. The second and third modules are a sequential stress analysis using FE-Implicit and FE-Explicit respectively. User-material subroutine is used to model the Viscoelastic properties of the material based on theory of micromechanics.

Virtual Manufacturing of Composite Structures Applying Implicit and Explicit FE Techniques

Virtual manufacturing of composites can yield an initial early estimation of the induced residual thermal stresses that affect component fatigue life, and deformations that affect required tolerances for assembly. Based on these estimation, the designer can make early decisions, which can help in reducing cost, regarding changes in part design or material properties. In this paper, an approach is proposed to simulate the autoclave manufacturing technique for unidirectional composites. The proposed approach consists of three modules. The first module is a Thermochemical model to estimate temperature and the degree of cure distributions in the composite part during the cure cycle. The second and third modules are stress analysis using FE-Implicit and FE-Explicit respectively. User-material subroutine will be used to model the Viscoelastic properties of the material based on micromechanical theory. Estimated deformation of the composite part can be corrected during the autoclave process by modifying the process-tool design. The deformed composite surface is sent to CATIA for design modification of the process-tool.

Accidental release of hazardous gases: modelling and assessing risk

The renewed concern in assessing risks and consequences from technological hazards in industrial and urban areas continues emphasizing the development of local-scale consequence analysis (CA) modelling tools able to predict shortterm pollution episodes and exposure effects on humans and the environment in case of accident with hazardous gases (hazmat). In this context, the main objective of this thesis is the development and validation of the EFfects of Released Hazardous gAses (EFRHA) model. This modelling tool is designed to simulate the outflow and atmospheric dispersion of heavy and passive hazmat gases in complex and build-up areas, and to estimate the exposure consequences of short-term pollution episodes in accordance to regulatory/safety threshold limits. Five main modules comprising up-to-date methods constitute the model: meteorological, terrain, source term, dispersion, and effects modules. Different initial physical states accident scenarios can be examined. Considered the main core of the developed tool, the dispersion module comprises a shallow layer modelling approach capable to account the main influence of obstacles during the hazmat gas dispersion phenomena. Model validation includes qualitative and quantitative analyses of main outputs by the comparison of modelled results against measurements and/or modelled databases. The preliminary analysis of meteorological and source term modules against modelled outputs from extensively validated models shows the consistent description of ambient conditions and the variation of the hazmat gas release. Dispersion is compared against measurements observations in obstructed and unobstructed areas for different release and dispersion scenarios. From the performance validation exercise, acceptable agreement was obtained, showing the reasonable numerical representation of measured features. In general, quality metrics are within or close to the acceptance limits recommended for ‘non-CFD models’, demonstrating its capability to reasonably predict hazmat gases accidental release and atmospheric dispersion in industrial and urban areas. EFRHA model was also applied to a particular case study, the Estarreja Chemical Complex (ECC), for a set of accidental release scenarios within a CA scope. The results show the magnitude of potential effects on the surrounding populated area and influence of the type of accident and the environment on the main outputs. Overall the present thesis shows that EFRHA model can be used as a straightforward tool to support CA studies in the scope of training and planning, but also, to support decision and emergency response in case of hazmat gases accidental release in industrial and built-up areas.

A Categorical Framework for the Specification and the Verification of Aspect Oriented Systems

Un objectif principal du génie logiciel est de pouvoir produire des logiciels complexes, de grande taille et fiables en un temps raisonnable. La technologie orientée objet (OO) a fourni de bons concepts et des techniques de modélisation et de programmation qui ont permis de développer des applications complexes tant dans le monde académique que dans le monde industriel. Cette expérience a cependant permis de découvrir les faiblesses du paradigme objet (par exemples, la dispersion de code et le problème de traçabilité). La programmation orientée aspect (OA) apporte une solution simple aux limitations de la programmation OO, telle que le problème des préoccupations transversales. Ces préoccupations transversales se traduisent par la dispersion du même code dans plusieurs modules du système ou l’emmêlement de plusieurs morceaux de code dans un même module. Cette nouvelle méthode de programmer permet d’implémenter chaque problématique indépendamment des autres, puis de les assembler selon des règles bien définies. La programmation OA promet donc une meilleure productivité, une meilleure réutilisation du code et une meilleure adaptation du code aux changements. Très vite, cette nouvelle façon de faire s’est vue s’étendre sur tout le processus de développement de logiciel en ayant pour but de préserver la modularité et la traçabilité, qui sont deux propriétés importantes des logiciels de bonne qualité. Cependant, la technologie OA présente de nombreux défis. Le raisonnement, la spécification, et la vérification des programmes OA présentent des difficultés d’autant plus que ces programmes évoluent dans le temps. Par conséquent, le raisonnement modulaire de ces programmes est requis sinon ils nécessiteraient d’être réexaminés au complet chaque fois qu’un composant est changé ou ajouté. Il est cependant bien connu dans la littérature que le raisonnement modulaire sur les programmes OA est difficile vu que les aspects appliqués changent souvent le comportement de leurs composantes de base [47]. Ces mêmes difficultés sont présentes au niveau des phases de spécification et de vérification du processus de développement des logiciels. Au meilleur de nos connaissances, la spécification modulaire et la vérification modulaire sont faiblement couvertes et constituent un champ de recherche très intéressant. De même, les interactions entre aspects est un sérieux problème dans la communauté des aspects. Pour faire face à ces problèmes, nous avons choisi d’utiliser la théorie des catégories et les techniques des spécifications algébriques. Pour apporter une solution aux problèmes ci-dessus cités, nous avons utilisé les travaux de Wiels [110] et d’autres contributions telles que celles décrites dans le livre [25]. Nous supposons que le système en développement est déjà décomposé en aspects et classes. La première contribution de notre thèse est l’extension des techniques des spécifications algébriques à la notion d’aspect. Deuxièmement, nous avons défini une logique, LA , qui est utilisée dans le corps des spécifications pour décrire le comportement de ces composantes. La troisième contribution consiste en la définition de l’opérateur de tissage qui correspond à la relation d’interconnexion entre les modules d’aspect et les modules de classe. La quatrième contribution concerne le développement d’un mécanisme de prévention qui permet de prévenir les interactions indésirables dans les systèmes orientés aspect.

Collaboration between infection control and occupational health in three continents: a success story with international impact

Globalization has been accompanied by the rapid spread of infectious diseases, and further strain on working conditions for health workers globally. Post-SARS, Canadian occupational health and infection control researchers got together to study how to better protect health workers, and found that training was indeed perceived as key to a positive safety culture. This led to developing information and communication technology (ICT) tools. The research conducted also showed the need for better workplace inspections, so a workplace audit tool was also developed to supplement worker questionnaires and the ICT. When invited to join Ecuadorean colleagues to promote occupational health and infection control, these tools were collectively adapted and improved, including face-to-face as well as on-line problem-based learning scenarios. The South African government then invited the team to work with local colleagues to improve occupational health and infection control, resulting in an improved web-based health information system to track incidents, exposures, and occupational injury and diseases. As the H1N1 pandemic struck, the online infection control course was adapted and translated into Spanish, as was a novel skill-building learning tool that permits health workers to practice selecting personal protective equipment. This tool was originally developed in collaboration with the countries from the Caribbean region and the Pan American Health Organization (PAHO). Research from these experiences led to strengthened focus on building capacity of health and safety committees, and new modules are thus being created, informed by that work. The products developed have been widely heralded as innovative and interactive, leading to their inclusion into “toolkits” used internationally. The tools used in Canada were substantially improved from the collaborative adaptation process for South and Central America and South Africa. This international collaboration between occupational health and infection control researchers led to the improvement of the research framework and development of tools, guidelines and information systems. Furthermore, the research and knowledge-transfer experience highlighted the value of partnership amongst Northern and Southern researchers in terms of sharing resources, experiences and knowledge.

Proposal of redundant drive wire mechanism for producing motions with high acceleration and high precision

A new wire mechanism called Redundant Drive Wire Mechanism (RDWM) is proposed. The purpose of this paper is to build up the theory of a RDWM with fast motion and fine motion. First, the basic concepts of the proposed mechanism is presented. Second, the vector closure condition for the proposed mechanism is developed. Next, we present the basic equations, propose the basic structure of RDWM with the Internal DOF module, Double Actuation Modules and Precision Modules together with the properties of the mechanism. Finally, we conduct the simulation to show the validity of the RDWM.

A rare structure at the syntax-discourse interface: heritage and Spanish-dominant native speakers weigh in

The present study examines knowledge of the discourse-appropriateness of Clitic Right Dislocation (CLRD) in a population of Heritage (HS) and Spanish-dominant Native Speakers in order to test the predictions of the Interface Hypothesis (IH; Sorace 2011). The IH predicts that speakers in language contact situations will experience difficulties with integrating information involving the interface of syntax and discourse modules. CLRD relates a dislocated constituent to a discourse antecedent, requiring integration of syntax and pragmatics. Results from an acceptability judgment task did not support the predictions of the IH. No statistical differences between the HSs’ performance and that of L1-dominant native speakers were evidenced when participants were presented with an offline task. Thus, our study did not find any evidence of “incomplete acquisition” (Montrul 2008) as it pertains to this specific linguistic structure.

Module property verification : A method to plan and perform quality verifications in modular architectures

Modular product architectures have generated numerous benefits for companies in terms of cost, lead-time and quality. The defined interfaces and the module’s properties decrease the effort to develop new product variants, and provide an opportunity to perform parallel tasks in design, manufacturing and assembly. The background of this thesis is that companies perform verifications (tests, inspections and controls) of products late, when most of the parts have been assembled. This extends the lead-time to delivery and ruins benefits from a modular product architecture; specifically when the verifications are extensive and the frequency of detected defects is high. Due to the number of product variants obtained from the modular product architecture, verifications must handle a wide range of equipment, instructions and goal values to ensure that high quality products can be delivered. As a result, the total benefits from a modular product architecture are difficult to achieve. This thesis describes a method for planning and performing verifications within a modular product architecture. The method supports companies by utilizing the defined modules for verifications already at module level, so called MPV (Module Property Verification). With MPV, defects are detected at an earlier point, compared to verification of a complete product, and the number of verifications is decreased. The MPV method is built up of three phases. In Phase A, candidate modules are evaluated on the basis of costs and lead-time of the verifications and the repair of defects. An MPV-index is obtained which quantifies the module and indicates if the module should be verified at product level or by MPV. In Phase B, the interface interaction between the modules is evaluated, as well as the distribution of properties among the modules. The purpose is to evaluate the extent to which supplementary verifications at product level is needed. Phase C supports a selection of the final verification strategy. The cost and lead-time for the supplementary verifications are considered together with the results from Phase A and B. The MPV method is based on a set of qualitative and quantitative measures and tools which provide an overview and support the achievement of cost and time efficient company specific verifications. A practical application in industry shows how the MPV method can be used, and the subsequent benefits

Characterization of the MEK5-ERK5 module in human neutrophils and its relationship to ERK1/ERK2 in the chemotactic response

The role of the extracellular signal-regulated kinase (ERK) 1 and ERK2 in the neutrophil chemotactic response remains to be identified since a previously used specific inhibitor of MEK1 and MEK2, PD98059, that was used to provide evidence for a role of ERK1 and ERK2 in regulating chemotaxis, has recently been reported to also inhibit MEK5. This issue is made more critical by our present finding that human neutrophils express mitogen-activated protein (MAP) kinase/ERK kinase (MEK)5 and ERK5 (Big MAP kinase), and that their activities were stimulated by the bacterial tripeptide, formyl methionyl-leucyl-phenylalanine (fMLP). Dose response studies demonstrated a bell-shaped profile of fMLP-stimulated MEK5 and ERK5 activation, but this was left-shifted when compared with the profile of fMLP-stimulated chemotaxis. Kinetics studies demonstrated increases in kinase activity within 2 min, peaking at 3–5 min, and MEK5 activation was more persistent than that of ERK5. There were some similarities as well as differences in the pattern of activation between fMLP-stimulated ERK1 and ERK2, and MEK5-ERK5 activation. The up-regulation of MEK5-ERK5 activities was dependent on phosphatidylinositol 3-kinase. Studies with the recently described specific MEK inhibitor, PD184352, at concentrations that inhibited ERK1 and ERK2 but not ERK5 activity demonstrate that the ERK1 and ERK2 modules were involved in regulating fMLP-stimulated chemotaxis and chemokinesis. Our data suggest that the MEK5-ERK5 module is likely to regulate neutrophil responses at very low chemoattractant concentrations whereas at higher concentrations, a shift to the ERK1/ERK2 and p38 modules is apparent.

International network for food and obesity/NCD research, monitoring and action support: benchmarking food environments towards healthier diets

Background and objectives: 

Structural and optical properties of CaTiO3 perovskite-based materials obtained by microwave-assisted hydrothermal synthesis: An experimental and theoretical insight

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Development of an integrative cessation program for co-smokers of cigarettes and cannabis: demand analysis, program description, and acceptability

Abstract Background Tobacco and cannabis use are strongly interrelated, but current national and international cessation programs typically focus on one substance, and address the other substance either only marginally or not at all. This study aimed to identify the demand for, and describe the development and content of, the first integrative group cessation program for co-smokers of cigarettes and cannabis. Methods First, a preliminary study using expert interviews, user focus groups with (ex-)smokers, and an online survey was conducted to investigate the demand for, and potential content of, an integrative smoking cessation program (ISCP) for tobacco and cannabis co-smokers. This study revealed that both experts and co-smokers considered an ISCP to be useful but expected only modest levels of readiness for participation.Based on the findings of the preliminary study, an interdisciplinary expert team developed a course concept and a recruitment strategy. The developed group cessation program is based on current treatment techniques (such as motivational interviewing, cognitive behavioural therapy, and self-control training) and structured into six course sessions.The program was evaluated regarding its acceptability among participants and course instructors. Results Both the participants and course instructors evaluated the course positively. Participants and instructors especially appreciated the group discussions and the modules that were aimed at developing personal strategies that could be applied during simultaneous cessation of tobacco and cannabis, such as dealing with craving, withdrawal, and high-risk situations. Conclusions There is a clear demand for a double cessation program for co-users of cigarettes and cannabis, and the first group cessation program tailored for these users has been developed and evaluated for acceptability. In the near future, the feasibility of the program will be evaluated. Trial registration Current Controlled Trials ISRCTN15248397