Architectures for Context Aware Services in Smart Environments

This thesis deals with Context Aware Services, Smart Environments, Context Management and solutions for Devices and Service Interoperability. Multi-vendor devices offer an increasing number of services and end-user applications that base their value on the ability to exploit the information originating from the surrounding environment by means of an increasing number of embedded sensors, e.g. GPS, compass, RFID readers, cameras and so on. However, usually such devices are not able to exchange information because of the lack of a shared data storage and common information exchange methods. A large number of standards and domain specific building blocks are available and are heavily used in today's products. However, the use of these solutions based on ready-to-use modules is not without problems. The integration and cooperation of different kinds of modules can be daunting because of growing complexity and dependency. In this scenarios it might be interesting to have an infrastructure that makes the coexistence of multi-vendor devices easy, while enabling low cost development and smooth access to services. This sort of technologies glue should reduce both software and hardware integration costs by removing the trouble of interoperability. The result should also lead to faster and simplified design, development and, deployment of cross-domain applications. This thesis is mainly focused on SW architectures supporting context aware service providers especially on the following subjects: - user preferences service adaptation - context management - content management - information interoperability - multivendor device interoperability - communication and connectivity interoperability Experimental activities were carried out in several domains including Cultural Heritage, indoor and personal smart spaces – all of which are considered significant test-beds in Context Aware Computing. The work evolved within european and national projects: on the europen side, I carried out my research activity within EPOCH, the FP6 Network of Excellence on “Processing Open Cultural Heritage” and within SOFIA, a project of the ARTEMIS JU on embedded systems. I worked in cooperation with several international establishments, including the University of Kent, VTT (the Technical Reserarch Center of Finland) and Eurotech. On the national side I contributed to a one-to-one research contract between ARCES and Telecom Italia. The first part of the thesis is focused on problem statement and related work and addresses interoperability issues and related architecture components. The second part is focused on specific architectures and frameworks: - MobiComp: a context management framework that I used in cultural heritage applications - CAB: a context, preference and profile based application broker which I designed within EPOCH Network of Excellence - M3: "Semantic Web based" information sharing infrastructure for smart spaces designed by Nokia within the European project SOFIA - NoTa: a service and transport independent connectivity framework - OSGi: the well known Java based service support framework The final section is dedicated to the middleware, the tools and, the SW agents developed during my Doctorate time to support context-aware services in smart environments.

Enabling a direct path from end-user specifications to executable protocols in a biology laboratory environment

Biomedical analyses are becoming increasingly complex, with respect to both the type of the data to be produced and the procedures to be executed. This trend is expected to continue in the future. The development of information and protocol management systems that can sustain this challenge is therefore becoming an essential enabling factor for all actors in the field. The use of custom-built solutions that require the biology domain expert to acquire or procure software engineering expertise in the development of the laboratory infrastructure is not fully satisfactory because it incurs undesirable mutual knowledge dependencies between the two camps. We propose instead an infrastructure concept that enables the domain experts to express laboratory protocols using proper domain knowledge, free from the incidence and mediation of the software implementation artefacts. In the system that we propose this is made possible by basing the modelling language on an authoritative domain specific ontology and then using modern model-driven architecture technology to transform the user models in software artefacts ready for execution in a multi-agent based execution platform specialized for biomedical laboratories.

Nondestructive evaluation of concrete compression strength by means of Artificial Neural Network (ANN)

The evaluation of structural performance of existing concrete buildings, built according to standards and materials quite different to those available today, requires procedures and methods able to cover lack of data about mechanical material properties and reinforcement detailing. To this end detailed inspections and test on materials are required. As a consequence tests on drilled cores are required; on the other end, it is stated that non-destructive testing (NDT) cannot be used as the only mean to get structural information, but can be used in conjunction with destructive testing (DT) by a representative correlation between DT and NDT. The aim of this study is to verify the accuracy of some formulas of correlation available in literature between measured parameters, i.e. rebound index, ultrasonic pulse velocity and compressive strength (SonReb Method). To this end a relevant number of DT and NDT tests has been performed on many school buildings located in Cesena (Italy). The above relationships have been assessed on site correlating NDT results to strength of core drilled in adjacent locations. Nevertheless, concrete compressive strength assessed by means of NDT methods and evaluated with correlation formulas has the advantage of being able to be implemented and used for future applications in a much more simple way than other methods, even if its accuracy is strictly limited to the analysis of concretes having the same characteristics as those used for their calibration. This limitation warranted a search for a different evaluation method for the non-destructive parameters obtained on site. To this aim, the methodology of neural identification of compressive strength is presented. Artificial Neural Network (ANN) suitable for the specific analysis were chosen taking into account the development presented in the literature in this field. The networks were trained and tested in order to detect a more reliable strength identification methodology.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

EXAM-S: an Analysis tool for Multi-Domain Policy Sets

As distributed collaborative applications and architectures are adopting policy based management for tasks such as access control, network security and data privacy, the management and consolidation of a large number of policies is becoming a crucial component of such policy based systems. In large-scale distributed collaborative applications like web services, there is the need of analyzing policy interactions and integrating policies. In this thesis, we propose and implement EXAM-S, a comprehensive environment for policy analysis and management, which can be used to perform a variety of functions such as policy property analyses, policy similarity analysis, policy integration etc. As part of this environment, we have proposed and implemented new techniques for the analysis of policies that rely on a deep study of state of the art techniques. Moreover, we propose an approach for solving heterogeneity problems that usually arise when considering the analysis of policies belonging to different domains. Our work focuses on analysis of access control policies written in the dialect of XACML (Extensible Access Control Markup Language). We consider XACML policies because XACML is a rich language which can represent many policies of interest to real world applications and is gaining widespread adoption in the industry.

Structural and functional analysis of centromeric chromatin

Animal neocentromeres are defined as ectopic centromeres that have formed in non-centromeric locations and avoid some of the features, like the DNA satellite sequence, that normally characterize canonical centromeres. Despite this, they are stable functional centromeres inherited through generations. The only existence of neocentromeres provide convincing evidence that centromere specification is determined by epigenetic rather than sequence-specific mechanisms. For all this reasons, we used them as simplified models to investigate the molecular mechanisms that underlay the formation and the maintenance of functional centromeres. We collected human cell lines carrying neocentromeres in different positions. To investigate the region involved in the process at the DNA sequence level we applied a recent technology that integrates Chromatin Immuno-Precipitation and DNA microarrays (ChIP-on-chip) using rabbit polyclonal antibodies directed against CENP-A or CENP-C human centromeric proteins. These DNA binding-proteins are required for kinetochore function and are exclusively targeted to functional centromeres. Thus, the immunoprecipitation of DNA bound by these proteins allows the isolation of centromeric sequences, including those of the neocentromeres. Neocentromeres arise even in protein-coding genes region. We further analyzed if the increased scaffold attachment sites and the corresponding tighter chromatin of the region involved in the neocentromerization process still were permissive or not to transcription of within encoded genes. Centromere repositioning is a phenomenon in which a neocentromere arisen without altering the gene order, followed by the inactivation of the canonical centromere, becomes fixed in population. It is a process of chromosome rearrangement fundamental in evolution, at the bases of speciation. The repeat-free region where the neocentromere initially forms, progressively acquires extended arrays of satellite tandem repeats that may contribute to its functional stability. In this view our attention focalized to the repositioned horse ECA11 centromere. ChIP-on-chip analysis was used to define the region involved and SNPs studies, mapping within the region involved into neocentromerization, were carried on. We have been able to describe the structural polymorphism of the chromosome 11 centromeric domain of Caballus population. That polymorphism was seen even between homologues chromosome of the same cells. That discovery was the first described ever. Genomic plasticity had a fundamental role in evolution. Centromeres are not static packaged region of genomes. The key question that fascinates biologists is to understand how that centromere plasticity could be combined to the stability and maintenance of centromeric function. Starting from the epigenetic point of view that underlies centromere formation, we decided to analyze the RNA content of centromeric chromatin. RNA, as well as secondary chemically modifications that involve both histones and DNA, represents a good candidate to guide somehow the centromere formation and maintenance. Many observations suggest that transcription of centromeric DNA or of other non-coding RNAs could affect centromere formation. To date has been no thorough investigation addressing the identity of the chromatin-associated RNAs (CARs) on a global scale. This prompted us to develop techniques to identify CARs in a genome-wide approach using high-throughput genomic platforms. The future goal of this study will be to focalize the attention on what strictly happens specifically inside centromere chromatin.