Diversity and characterisation of coagulasenegative staphylococci isolated from healthy individuals in Portugal

In the past few years the interest in coagulase-negative staphylococci (CoNS) has significantly increased in human medicine. CoNS are common commensal colonisers of the human skin, although now also recognised as major nosocomial pathogens. Over the last decades, several studies have been carried out in order to understand the pathogenicity mechanisms of CoNS. The well known determinants in the pathogenesis of CoNS infections are their ability to form biofilms and an exceptional resistance to several antibiotics. Nevertheless, there is a lack of studies regarding the commensal lifestyle of these microorganisms. Additionally, it is now hypothesised that commensal bacteria might be a reservoir of pathogenic determinants. Therefore, the work described throughout this thesis was aimed to perform a phenotypic and genotypic characterisation of different CoNS species isolated from healthy Portuguese individuals. A total of 61 CoNS isolates, comprising 7 different species, were obtained and characterised at the level of biofilm formation and antibiotic susceptibility profiles. According to the results, biofilm formation ability and presence of biofilm-associated genes were commonly found features, highlighting their pivotal role in the colonising lifestyle of CoNS. This study also addressed the correlation between phenotypic and genotypic characteristics of biofilm formation, corroborating and raising questions about the importance of some genes in this process. Moreover, it was observed a great proportion of isolates with decreased susceptibility and multiple resistances to some important antibiotics. A significant association between antibiotic resistance and biofilm formation was also demonstrated, and some hypotheses about the nature of such association were provided. Lastly, the expression patterns of two biofilm-associated genes at two distinct biofilm developmental stages were determined, confirming their importance in the accumulative stage of biofilm formation. Overall, the results presented in this thesis indicate that staphylococcal skin flora might be an important reservoir of potentially pathogenic bacteria and, simultaneously, bring to light new perceptions about the molecular basis of staphylococcal biofilm formation, and the nature of the association between antibiotic resistance and biofilm formation.

A compositional scheduling framework for digital avionics systems

ARINC specification 653-2 describes the interface between application software and underlying middleware in a distributed real-time avionics system. The real-time workload in this system comprises of partitions, where each partition consists of one or more processes. Processes incur blocking and preemption overheads and can communicate with other processes in the system. In this work we develop compositional techniques for automated scheduling of such partitions and processes. At present, system designers manually schedule partitions based on interactions they have with the partition vendors. This approach is not only time consuming, but can also result in under utilization of resources. In contrast, the technique proposed in this paper is a principled approach for scheduling ARINC-653 partitions and therefore should facilitate system integration.

Compositional multiprocessor scheduling: the GMPR interface

Composition is a practice of key importance in software engineering. When real-time applications are composed, it is necessary that their timing properties (such as meeting the deadlines) are guaranteed. The composition is performed by establishing an interface between the application and the physical platform. Such an interface typically contains information about the amount of computing capacity needed by the application. For multiprocessor platforms, the interface should also present information about the degree of parallelism. Several interface proposals have recently been put forward in various research works. However, those interfaces are either too complex to be handled or too pessimistic. In this paper we propose the generalized multiprocessor periodic resource model (GMPR) that is strictly superior to the MPR model without requiring a too detailed description. We then derive a method to compute the interface from the application specification. This method has been implemented in Matlab routines that are publicly available.