Semantic Publishing: issues, solutions and new trends in scholarly publishing within the Semantic Web era

This work is concerned with the increasing relationships between two distinct multidisciplinary research fields, Semantic Web technologies and scholarly publishing, that in this context converge into one precise research topic: Semantic Publishing. In the spirit of the original aim of Semantic Publishing, i.e. the improvement of scientific communication by means of semantic technologies, this thesis proposes theories, formalisms and applications for opening up semantic publishing to an effective interaction between scholarly documents (e.g., journal articles) and their related semantic and formal descriptions. In fact, the main aim of this work is to increase the users' comprehension of documents and to allow document enrichment, discovery and linkage to document-related resources and contexts, such as other articles and raw scientific data. In order to achieve these goals, this thesis investigates and proposes solutions for three of the main issues that semantic publishing promises to address, namely: the need of tools for linking document text to a formal representation of its meaning, the lack of complete metadata schemas for describing documents according to the publishing vocabulary, and absence of effective user interfaces for easily acting on semantic publishing models and theories.

Cooperative communication and distributed detection in wireless sensor networks

Recent progress in microelectronic and wireless communications have enabled the development of low cost, low power, multifunctional sensors, which has allowed the birth of new type of networks named wireless sensor networks (WSNs). The main features of such networks are: the nodes can be positioned randomly over a given field with a high density; each node operates both like sensor (for collection of environmental data) as well as transceiver (for transmission of information to the data retrieval); the nodes have limited energy resources. The use of wireless communications and the small size of nodes, make this type of networks suitable for a large number of applications. For example, sensor nodes can be used to monitor a high risk region, as near a volcano; in a hospital they could be used to monitor physical conditions of patients. For each of these possible application scenarios, it is necessary to guarantee a trade-off between energy consumptions and communication reliability. The thesis investigates the use of WSNs in two possible scenarios and for each of them suggests a solution that permits to solve relating problems considering the trade-off introduced. The first scenario considers a network with a high number of nodes deployed in a given geographical area without detailed planning that have to transmit data toward a coordinator node, named sink, that we assume to be located onboard an unmanned aerial vehicle (UAV). This is a practical example of reachback communication, characterized by the high density of nodes that have to transmit data reliably and efficiently towards a far receiver. It is considered that each node transmits a common shared message directly to the receiver onboard the UAV whenever it receives a broadcast message (triggered for example by the vehicle). We assume that the communication channels between the local nodes and the receiver are subject to fading and noise. The receiver onboard the UAV must be able to fuse the weak and noisy signals in a coherent way to receive the data reliably. It is proposed a cooperative diversity concept as an effective solution to the reachback problem. In particular, it is considered a spread spectrum (SS) transmission scheme in conjunction with a fusion center that can exploit cooperative diversity, without requiring stringent synchronization between nodes. The idea consists of simultaneous transmission of the common message among the nodes and a Rake reception at the fusion center. The proposed solution is mainly motivated by two goals: the necessity to have simple nodes (to this aim we move the computational complexity to the receiver onboard the UAV), and the importance to guarantee high levels of energy efficiency of the network, thus increasing the network lifetime. The proposed scheme is analyzed in order to better understand the effectiveness of the approach presented. The performance metrics considered are both the theoretical limit on the maximum amount of data that can be collected by the receiver, as well as the error probability with a given modulation scheme. Since we deal with a WSN, both of these performance are evaluated taking into consideration the energy efficiency of the network. The second scenario considers the use of a chain network for the detection of fires by using nodes that have a double function of sensors and routers. The first one is relative to the monitoring of a temperature parameter that allows to take a local binary decision of target (fire) absent/present. The second one considers that each node receives a decision made by the previous node of the chain, compares this with that deriving by the observation of the phenomenon, and transmits the final result to the next node. The chain ends at the sink node that transmits the received decision to the user. In this network the goals are to limit throughput in each sensor-to-sensor link and minimize probability of error at the last stage of the chain. This is a typical scenario of distributed detection. To obtain good performance it is necessary to define some fusion rules for each node to summarize local observations and decisions of the previous nodes, to get a final decision that it is transmitted to the next node. WSNs have been studied also under a practical point of view, describing both the main characteristics of IEEE802:15:4 standard and two commercial WSN platforms. By using a commercial WSN platform it is realized an agricultural application that has been tested in a six months on-field experimentation.

Forma breve e fotografia: una narrativa del Mozambico

La relazione interdisciplinare tra letteratura e fotografia, nella rilettura della storia recente del Mozambico, è l’oggetto di studio della presente tesi. Il presupposto coincide in primo luogo con la disamina interna della dialettica esistente tra archivio coloniale e oralità, modalità narrativa in parte transitata nella estória, declinazione lusofona della forma breve che permette di recuperare l’eredità popolare del racconto tradizionale. Il dialogo tra verbale e visuale consente a sua volta di stabilire nuovi paradigmi interpretativi nel dibattito postcoloniale tra memoria, trauma e rappresentazione. L’analisi comparativa tra la narrativa di João Paulo Borges Coelho e la fotografia di Ricardo Rangel rivela sguardi diversi sul mondo circostante, ma anche convergenze contemplative che si completano nell’incorporazione reciproca delle “omologie strutturali” comuni alle due modalità espressive. La fotografia colma delle lacune fornendoci delle visioni del passato, ma, in quanto “rappresentazione”, ci mostra il mondo per come appare e non per come funziona. Il testo letterario, grazie al suo approccio dialogico-narrativo, consente la rielaborazione museologica della complessa pletora di interferenze semantiche e culturali racchiuse nelle immagini, in altre parole fornisce degli “indizi di verità” da cui (ri)partire per l’elaborazione di nuovi archetipi narrativi tra l’evento rappresentato e la Storia di cui fa parte. Il punto di tangenza tra i due linguaggi è la cornice, espediente fotografico e narrativo che permette di tracciare i confini tra l’indicibile e l’invisibile, ma anche tra ciò che si narra e ciò che sta fuori dalla narrazione, ovvero fuori dalla storia. La tensione dialettica che si instaura tra questi due universi è seminale per stabilire le ragioni della specificità letteraria mozambicana perché, come afferma Luandino Vieira, “nel contesto postcoloniale gli scrittori sono dei satelliti che ruotano intorno ai «buchi neri della storia» la cui forza di attrazione permette la riorganizzazione dell’intero universo letterario.

Knowledge Patterns for the Web: extraction, tranformation and reuse

This thesis aims at investigating methods and software architectures for discovering what are the typical and frequently occurring structures used for organizing knowledge in the Web. We identify these structures as Knowledge Patterns (KPs). KP discovery needs to address two main research problems: the heterogeneity of sources, formats and semantics in the Web (i.e., the knowledge soup problem) and the difficulty to draw relevant boundary around data that allows to capture the meaningful knowledge with respect to a certain context (i.e., the knowledge boundary problem). Hence, we introduce two methods that provide different solutions to these two problems by tackling KP discovery from two different perspectives: (i) the transformation of KP-like artifacts to KPs formalized as OWL2 ontologies; (ii) the bottom-up extraction of KPs by analyzing how data are organized in Linked Data. The two methods address the knowledge soup and boundary problems in different ways. The first method provides a solution to the two aforementioned problems that is based on a purely syntactic transformation step of the original source to RDF followed by a refactoring step whose aim is to add semantics to RDF by select meaningful RDF triples. The second method allows to draw boundaries around RDF in Linked Data by analyzing type paths. A type path is a possible route through an RDF that takes into account the types associated to the nodes of a path. Then we present K~ore, a software architecture conceived to be the basis for developing KP discovery systems and designed according to two software architectural styles, i.e, the Component-based and REST. Finally we provide an example of reuse of KP based on Aemoo, an exploratory search tool which exploits KPs for performing entity summarization.

Assimilation of Meteosat Second Generation (MSG) satellite data in a regional numerical weather prediction model using a one-dimensional variational approach

The quality of temperature and humidity retrievals from the infrared SEVIRI sensors on the geostationary Meteosat Second Generation (MSG) satellites is assessed by means of a one dimensional variational algorithm. The study is performed with the aim of improving the spatial and temporal resolution of available observations to feed analysis systems designed for high resolution regional scale numerical weather prediction (NWP) models. The non-hydrostatic forecast model COSMO (COnsortium for Small scale MOdelling) in the ARPA-SIM operational configuration is used to provide background fields. Only clear sky observations over sea are processed. An optimised 1D–VAR set-up comprising of the two water vapour and the three window channels is selected. It maximises the reduction of errors in the model backgrounds while ensuring ease of operational implementation through accurate bias correction procedures and correct radiative transfer simulations. The 1D–VAR retrieval quality is firstly quantified in relative terms employing statistics to estimate the reduction in the background model errors. Additionally the absolute retrieval accuracy is assessed comparing the analysis with independent radiosonde and satellite observations. The inclusion of satellite data brings a substantial reduction in the warm and dry biases present in the forecast model. Moreover it is shown that the retrieval profiles generated by the 1D–VAR are well correlated with the radiosonde measurements. Subsequently the 1D–VAR technique is applied to two three–dimensional case–studies: a false alarm case–study occurred in Friuli–Venezia–Giulia on the 8th of July 2004 and a heavy precipitation case occurred in Emilia–Romagna region between 9th and 12th of April 2005. The impact of satellite data for these two events is evaluated in terms of increments in the integrated water vapour and saturation water vapour over the column, in the 2 meters temperature and specific humidity and in the surface temperature. To improve the 1D–VAR technique a method to calculate flow–dependent model error covariance matrices is also assessed. The approach employs members from an ensemble forecast system generated by perturbing physical parameterisation schemes inside the model. The improved set–up applied to the case of 8th of July 2004 shows a substantial neutral impact.

Mathematical models of cognitive processes

The research activity carried out during the PhD course was focused on the development of mathematical models of some cognitive processes and their validation by means of data present in literature, with a double aim: i) to achieve a better interpretation and explanation of the great amount of data obtained on these processes from different methodologies (electrophysiological recordings on animals, neuropsychological, psychophysical and neuroimaging studies in humans), ii) to exploit model predictions and results to guide future research and experiments. In particular, the research activity has been focused on two different projects: 1) the first one concerns the development of neural oscillators networks, in order to investigate the mechanisms of synchronization of the neural oscillatory activity during cognitive processes, such as object recognition, memory, language, attention; 2) the second one concerns the mathematical modelling of multisensory integration processes (e.g. visual-acoustic), which occur in several cortical and subcortical regions (in particular in a subcortical structure named Superior Colliculus (SC)), and which are fundamental for orienting motor and attentive responses to external world stimuli. This activity has been realized in collaboration with the Center for Studies and Researches in Cognitive Neuroscience of the University of Bologna (in Cesena) and the Department of Neurobiology and Anatomy of the Wake Forest University School of Medicine (NC, USA). PART 1. Objects representation in a number of cognitive functions, like perception and recognition, foresees distribute processes in different cortical areas. One of the main neurophysiological question concerns how the correlation between these disparate areas is realized, in order to succeed in grouping together the characteristics of the same object (binding problem) and in maintaining segregated the properties belonging to different objects simultaneously present (segmentation problem). Different theories have been proposed to address these questions (Barlow, 1972). One of the most influential theory is the so called “assembly coding”, postulated by Singer (2003), according to which 1) an object is well described by a few fundamental properties, processing in different and distributed cortical areas; 2) the recognition of the object would be realized by means of the simultaneously activation of the cortical areas representing its different features; 3) groups of properties belonging to different objects would be kept separated in the time domain. In Chapter 1.1 and in Chapter 1.2 we present two neural network models for object recognition, based on the “assembly coding” hypothesis. These models are networks of Wilson-Cowan oscillators which exploit: i) two high-level “Gestalt Rules” (the similarity and previous knowledge rules), to realize the functional link between elements of different cortical areas representing properties of the same object (binding problem); 2) the synchronization of the neural oscillatory activity in the γ-band (30-100Hz), to segregate in time the representations of different objects simultaneously present (segmentation problem). These models are able to recognize and reconstruct multiple simultaneous external objects, even in difficult case (some wrong or lacking features, shared features, superimposed noise). In Chapter 1.3 the previous models are extended to realize a semantic memory, in which sensory-motor representations of objects are linked with words. To this aim, the network, previously developed, devoted to the representation of objects as a collection of sensory-motor features, is reciprocally linked with a second network devoted to the representation of words (lexical network) Synapses linking the two networks are trained via a time-dependent Hebbian rule, during a training period in which individual objects are presented together with the corresponding words. Simulation results demonstrate that, during the retrieval phase, the network can deal with the simultaneous presence of objects (from sensory-motor inputs) and words (from linguistic inputs), can correctly associate objects with words and segment objects even in the presence of incomplete information. Moreover, the network can realize some semantic links among words representing objects with some shared features. These results support the idea that semantic memory can be described as an integrated process, whose content is retrieved by the co-activation of different multimodal regions. In perspective, extended versions of this model may be used to test conceptual theories, and to provide a quantitative assessment of existing data (for instance concerning patients with neural deficits). PART 2. The ability of the brain to integrate information from different sensory channels is fundamental to perception of the external world (Stein et al, 1993). It is well documented that a number of extraprimary areas have neurons capable of such a task; one of the best known of these is the superior colliculus (SC). This midbrain structure receives auditory, visual and somatosensory inputs from different subcortical and cortical areas, and is involved in the control of orientation to external events (Wallace et al, 1993). SC neurons respond to each of these sensory inputs separately, but is also capable of integrating them (Stein et al, 1993) so that the response to the combined multisensory stimuli is greater than that to the individual component stimuli (enhancement). This enhancement is proportionately greater if the modality-specific paired stimuli are weaker (the principle of inverse effectiveness). Several studies have shown that the capability of SC neurons to engage in multisensory integration requires inputs from cortex; primarily the anterior ectosylvian sulcus (AES), but also the rostral lateral suprasylvian sulcus (rLS). If these cortical inputs are deactivated the response of SC neurons to cross-modal stimulation is no different from that evoked by the most effective of its individual component stimuli (Jiang et al 2001). This phenomenon can be better understood through mathematical models. The use of mathematical models and neural networks can place the mass of data that has been accumulated about this phenomenon and its underlying circuitry into a coherent theoretical structure. In Chapter 2.1 a simple neural network model of this structure is presented; this model is able to reproduce a large number of SC behaviours like multisensory enhancement, multisensory and unisensory depression, inverse effectiveness. In Chapter 2.2 this model was improved by incorporating more neurophysiological knowledge about the neural circuitry underlying SC multisensory integration, in order to suggest possible physiological mechanisms through which it is effected. This endeavour was realized in collaboration with Professor B.E. Stein and Doctor B. Rowland during the 6 months-period spent at the Department of Neurobiology and Anatomy of the Wake Forest University School of Medicine (NC, USA), within the Marco Polo Project. The model includes four distinct unisensory areas that are devoted to a topological representation of external stimuli. Two of them represent subregions of the AES (i.e., FAES, an auditory area, and AEV, a visual area) and send descending inputs to the ipsilateral SC; the other two represent subcortical areas (one auditory and one visual) projecting ascending inputs to the same SC. Different competitive mechanisms, realized by means of population of interneurons, are used in the model to reproduce the different behaviour of SC neurons in conditions of cortical activation and deactivation. The model, with a single set of parameters, is able to mimic the behaviour of SC multisensory neurons in response to very different stimulus conditions (multisensory enhancement, inverse effectiveness, within- and cross-modal suppression of spatially disparate stimuli), with cortex functional and cortex deactivated, and with a particular type of membrane receptors (NMDA receptors) active or inhibited. All these results agree with the data reported in Jiang et al. (2001) and in Binns and Salt (1996). The model suggests that non-linearities in neural responses and synaptic (excitatory and inhibitory) connections can explain the fundamental aspects of multisensory integration, and provides a biologically plausible hypothesis about the underlying circuitry.

Application Platforms for the Internet of Things: Theory, Architecture, Protocols, Data Formats, and Privacy

The Internet of Things (IoT) is the next industrial revolution: we will interact naturally with real and virtual devices as a key part of our daily life. This technology shift is expected to be greater than the Web and Mobile combined. As extremely different technologies are needed to build connected devices, the Internet of Things field is a junction between electronics, telecommunications and software engineering. Internet of Things application development happens in silos, often using proprietary and closed communication protocols. There is the common belief that only if we can solve the interoperability problem we can have a real Internet of Things. After a deep analysis of the IoT protocols, we identified a set of primitives for IoT applications. We argue that each IoT protocol can be expressed in term of those primitives, thus solving the interoperability problem at the application protocol level. Moreover, the primitives are network and transport independent and make no assumption in that regard. This dissertation presents our implementation of an IoT platform: the Ponte project. Privacy issues follows the rise of the Internet of Things: it is clear that the IoT must ensure resilience to attacks, data authentication, access control and client privacy. We argue that it is not possible to solve the privacy issue without solving the interoperability problem: enforcing privacy rules implies the need to limit and filter the data delivery process. However, filtering data require knowledge of how the format and the semantics of the data: after an analysis of the possible data formats and representations for the IoT, we identify JSON-LD and the Semantic Web as the best solution for IoT applications. Then, this dissertation present our approach to increase the throughput of filtering semantic data by a factor of ten.

Il fascicolo sanitario elettronico tra Semantic Web e diritto alla privacy

Principale obiettivo della ricerca è quello di ricostruire lo stato dell’arte in materia di sanità elettronica e Fascicolo Sanitario Elettronico, con una precipua attenzione ai temi della protezione dei dati personali e dell’interoperabilità. A tal fine sono stati esaminati i documenti, vincolanti e non, dell’Unione europea nonché selezionati progetti europei e nazionali (come “Smart Open Services for European Patients” (EU); “Elektronische Gesundheitsakte” (Austria); “MedCom” (Danimarca); “Infrastruttura tecnologica del Fascicolo Sanitario Elettronico”, “OpenInFSE: Realizzazione di un’infrastruttura operativa a supporto dell’interoperabilità delle soluzioni territoriali di fascicolo sanitario elettronico nel contesto del sistema pubblico di connettività”, “Evoluzione e interoperabilità tecnologica del Fascicolo Sanitario Elettronico”, “IPSE - Sperimentazione di un sistema per l’interoperabilità europea e nazionale delle soluzioni di Fascicolo Sanitario Elettronico: componenti Patient Summary e ePrescription” (Italia)). Le analisi giuridiche e tecniche mostrano il bisogno urgente di definire modelli che incoraggino l’utilizzo di dati sanitari ed implementino strategie effettive per l’utilizzo con finalità secondarie di dati sanitari digitali , come Open Data e Linked Open Data. L’armonizzazione giuridica e tecnologica è vista come aspetto strategico per ridurre i conflitti in materia di protezione di dati personali esistenti nei Paesi membri nonché la mancanza di interoperabilità tra i sistemi informativi europei sui Fascicoli Sanitari Elettronici. A questo scopo sono state individuate tre linee guida: (1) armonizzazione normativa, (2) armonizzazione delle regole, (3) armonizzazione del design dei sistemi informativi. I principi della Privacy by Design (“prottivi” e “win-win”), così come gli standard del Semantic Web, sono considerate chiavi risolutive per il suddetto cambiamento.

Contribution of Non-Covalent Interactions and Electronic Effects on the Conformational Landscape and Tautomeric Equilibria of Molecules and Molecular Complexes: Structural and Dynamical Data from Rotational Spectroscopy

This thesis concerns the study of complex conformational surfaces and tautomeric equilibria of molecules and molecular complexes by quantum chemical methods and rotational spectroscopy techniques. In particular, the focus of this research is on the effects of substitution and noncovalent interactions in determining the energies and geometries of different conformers, tautomers or molecular complexes. The Free-Jet Absorption Millimeter Wave spectroscopy and the Pulsed-Jet Fourier Transform Microwave spectroscopy have been applied to perform these studies and the obtained results showcase the suitability of these techniques for the study of conformational surfaces and intermolecular interactions. The series of investigations of selected medium-size molecules and complexes have shown how different instrumental setups can be used to obtain a variety of results on molecular properties. The systems studied, include molecules of biological interest such as anethole and molecules of astrophysical interest such as N-methylaminoethanol. Moreover halogenation effects have been investigated on halogen substituted tautomeric systems (5-chlorohydroxypyridine and 6-chlorohydroxypyridine), where it has shown that the position of the inserted halogen atom affects the prototropic equilibrium. As for fluorination effects, interesting results have been achieved investigating some small complexes where a molecule of water is used as a probe to reveal the changes on the electrostatic potential of different fluorinated compounds: 2-fluoropyridine, 3-fluoropyridine and penta-fluoropyridine. While in the case of the molecular complex between water and 2-fluoropyridine and 3-fluoropyridine the geometry of the complex with one water molecule is analogous to that of pyridine with the water molecule linked to the pyridine nitrogen, the case of pentafluoropyridine reveals the effect of perfluorination and the water oxygen points towards the positive center of the pyridine ring. Additional molecular adducts with a molecule of water have been analyzed (benzylamine-water and acrylic acid-water) in order to reveal the stabilizing driving forces that characterize these complexes.

Searching and retrieving in content-based repositories of formal mathematical knowledge

In this thesis, the author presents a query language for an RDF (Resource Description Framework) database and discusses its applications in the context of the HELM project (the Hypertextual Electronic Library of Mathematics). This language aims at meeting the main requirements coming from the RDF community. in particular it includes: a human readable textual syntax and a machine-processable XML (Extensible Markup Language) syntax both for queries and for query results, a rigorously exposed formal semantics, a graph-oriented RDF data access model capable of exploring an entire RDF graph (including both RDF Models and RDF Schemata), a full set of Boolean operators to compose the query constraints, fully customizable and highly structured query results having a 4-dimensional geometry, some constructions taken from ordinary programming languages that simplify the formulation of complex queries. The HELM project aims at integrating the modern tools for the automation of formal reasoning with the most recent electronic publishing technologies, in order create and maintain a hypertextual, distributed virtual library of formal mathematical knowledge. In the spirit of the Semantic Web, the documents of this library include RDF metadata describing their structure and content in a machine-understandable form. Using the author's query engine, HELM exploits this information to implement some functionalities allowing the interactive and automatic retrieval of documents on the basis of content-aware requests that take into account the mathematical nature of these documents.