Sviluppo di un'applicazione bioinformatica per la gestione dei dati di antibiotico sensibilità di isolati clinici

Il problema dell'antibiotico-resistenza è un problema di sanità pubblica per affrontare il quale è necessario un sistema di sorveglianza basato sulla raccolta e l'analisi dei dati epidemiologici di laboratorio. Il progetto di dottorato è consistito nello sviluppo di una applicazione web per la gestione di tali dati di antibiotico sensibilità di isolati clinici utilizzabile a livello di ospedale. Si è creata una piattaforma web associata a un database relazionale per avere un’applicazione dinamica che potesse essere aggiornata facilmente inserendo nuovi dati senza dover manualmente modificare le pagine HTML che compongono l’applicazione stessa. E’ stato utilizzato il database open-source MySQL in quanto presenta numerosi vantaggi: estremamente stabile, elevate prestazioni, supportato da una grande comunità online ed inoltre gratuito. Il contenuto dinamico dell’applicazione web deve essere generato da un linguaggio di programmazione tipo “scripting” che automatizzi operazioni di inserimento, modifica, cancellazione, visualizzazione di larghe quantità di dati. E’ stato scelto il PHP, linguaggio open-source sviluppato appositamente per la realizzazione di pagine web dinamiche, perfettamente utilizzabile con il database MySQL. E’ stata definita l’architettura del database creando le tabelle contenenti i dati e le relazioni tra di esse: le anagrafiche, i dati relativi ai campioni, microrganismi isolati e agli antibiogrammi con le categorie interpretative relative al dato antibiotico. Definite tabelle e relazioni del database è stato scritto il codice associato alle funzioni principali: inserimento manuale di antibiogrammi, importazione di antibiogrammi multipli provenienti da file esportati da strumenti automatizzati, modifica/eliminazione degli antibiogrammi precedenti inseriti nel sistema, analisi dei dati presenti nel database con tendenze e andamenti relativi alla prevalenza di specie microbiche e alla chemioresistenza degli stessi, corredate da grafici. Lo sviluppo ha incluso continui test delle funzioni via via implementate usando reali dati clinici e sono stati introdotti appositi controlli e l’introduzione di una semplice e pulita veste grafica.

Interpreting Judgements using Knowledge Representation Methods and Computational Models of Argument

The goal of the present research is to define a Semantic Web framework for precedent modelling, by using knowledge extracted from text, metadata, and rules, while maintaining a strong text-to-knowledge morphism between legal text and legal concepts, in order to fill the gap between legal document and its semantics. The framework is composed of four different models that make use of standard languages from the Semantic Web stack of technologies: a document metadata structure, modelling the main parts of a judgement, and creating a bridge between a text and its semantic annotations of legal concepts; a legal core ontology, modelling abstract legal concepts and institutions contained in a rule of law; a legal domain ontology, modelling the main legal concepts in a specific domain concerned by case-law; an argumentation system, modelling the structure of argumentation. The input to the framework includes metadata associated with judicial concepts, and an ontology library representing the structure of case-law. The research relies on the previous efforts of the community in the field of legal knowledge representation and rule interchange for applications in the legal domain, in order to apply the theory to a set of real legal documents, stressing the OWL axioms definitions as much as possible in order to enable them to provide a semantically powerful representation of the legal document and a solid ground for an argumentation system using a defeasible subset of predicate logics. It appears that some new features of OWL2 unlock useful reasoning features for legal knowledge, especially if combined with defeasible rules and argumentation schemes. The main task is thus to formalize legal concepts and argumentation patterns contained in a judgement, with the following requirement: to check, validate and reuse the discourse of a judge - and the argumentation he produces - as expressed by the judicial text.

A communication infrastructure to support knowledge level agents on the web

Agent Communication Languages (ACLs) have been developed to provide a way for agents to communicate with each other supporting cooperation in Multi-Agent Systems. In the past few years many ACLs have been proposed for Multi-Agent Systems, such as KQML and FIPA-ACL. The goal of these languages is to support high-level, human like communication among agents, exploiting Knowledge Level features rather than symbol level ones. Adopting these ACLs, and mainly the FIPA-ACL specifications, many agent platforms and prototypes have been developed. Despite these efforts, an important issue in the research on ACLs is still open and concerns how these languages should deal (at the Knowledge Level) with possible failures of agents. Indeed, the notion of Knowledge Level cannot be straightforwardly extended to a distributed framework such as MASs, because problems concerning communication and concurrency may arise when several Knowledge Level agents interact (for example deadlock or starvation). The main contribution of this Thesis is the design and the implementation of NOWHERE, a platform to support Knowledge Level Agents on the Web. NOWHERE exploits an advanced Agent Communication Language, FT-ACL, which provides high-level fault-tolerant communication primitives and satisfies a set of well defined Knowledge Level programming requirements. NOWHERE is well integrated with current technologies, for example providing full integration for Web services. Supporting different middleware used to send messages, it can be adapted to various scenarios. In this Thesis we present the design and the implementation of the architecture, together with a discussion of the most interesting details and a comparison with other emerging agent platforms. We also present several case studies where we discuss the benefits of programming agents using the NOWHERE architecture, comparing the results with other solutions. Finally, the complete source code of the basic examples can be found in appendix.

On making web accessibility more accessible: strategy and tools for social good

The world currently faces a paradox in terms of accessibility for people with disabilities. While digital technologies hold immense potential to improve their quality of life, the majority of web content still exhibits critical accessibility issues. This PhD thesis addresses this challenge by proposing two interconnected research branches. The first introduces a groundbreaking approach to improving web accessibility by rethinking how it is approached, making it more accessible itself. It involves the development of: 1. AX, a declarative framework of web components that enforces the generation of accessible markup by means of static analysis. 2. An innovative accessibility testing and evaluation methodology, which communicates test results by exploiting concepts that developers are already familiar with (visual rendering and mouse operability) to convey the accessibility of a page. This methodology is implemented through the SAHARIAN browser extension. 3. A11A, a categorized and structured collection of curated accessibility resources aimed at facilitating their intended audiences discover and use them. The second branch focuses on unleashing the full potential of digital technologies to improve accessibility in the physical world. The thesis proposes the SCAMP methodology to make scientific artifacts accessible to blind, visually impaired individuals, and the general public. It enhances the natural characteristics of objects, making them more accessible through interactive, multimodal, and multisensory experiences. Additionally, the prototype of \gls{a11yvt}, a system supporting accessible virtual tours, is presented. It provides blind and visually impaired individuals with features necessary to explore unfamiliar indoor environments, while maintaining universal design principles that makes it suitable for usage by the general public. The thesis extensively discusses the theoretical foundations, design, development, and unique characteristics of these innovative tools. Usability tests with the intended target audiences demonstrate the effectiveness of the proposed artifacts, suggesting their potential to significantly improve the current state of accessibility.

User interaction widgets for interactive theorem proving

Matita (that means pencil in Italian) is a new interactive theorem prover under development at the University of Bologna. When compared with state-of-the-art proof assistants, Matita presents both traditional and innovative aspects. The underlying calculus of the system, namely the Calculus of (Co)Inductive Constructions (CIC for short), is well-known and is used as the basis of another mainstream proof assistant—Coq—with which Matita is to some extent compatible. In the same spirit of several other systems, proof authoring is conducted by the user as a goal directed proof search, using a script for storing textual commands for the system. In the tradition of LCF, the proof language of Matita is procedural and relies on tactic and tacticals to proceed toward proof completion. The interaction paradigm offered to the user is based on the script management technique at the basis of the popularity of the Proof General generic interface for interactive theorem provers: while editing a script the user can move forth the execution point to deliver commands to the system, or back to retract (or “undo”) past commands. Matita has been developed from scratch in the past 8 years by several members of the Helm research group, this thesis author is one of such members. Matita is now a full-fledged proof assistant with a library of about 1.000 concepts. Several innovative solutions spun-off from this development effort. This thesis is about the design and implementation of some of those solutions, in particular those relevant for the topic of user interaction with theorem provers, and of which this thesis author was a major contributor. Joint work with other members of the research group is pointed out where needed. The main topics discussed in this thesis are briefly summarized below. Disambiguation. Most activities connected with interactive proving require the user to input mathematical formulae. Being mathematical notation ambiguous, parsing formulae typeset as mathematicians like to write down on paper is a challenging task; a challenge neglected by several theorem provers which usually prefer to fix an unambiguous input syntax. Exploiting features of the underlying calculus, Matita offers an efficient disambiguation engine which permit to type formulae in the familiar mathematical notation. Step-by-step tacticals. Tacticals are higher-order constructs used in proof scripts to combine tactics together. With tacticals scripts can be made shorter, readable, and more resilient to changes. Unfortunately they are de facto incompatible with state-of-the-art user interfaces based on script management. Such interfaces indeed do not permit to position the execution point inside complex tacticals, thus introducing a trade-off between the usefulness of structuring scripts and a tedious big step execution behavior during script replaying. In Matita we break this trade-off with tinycals: an alternative to a subset of LCF tacticals which can be evaluated in a more fine-grained manner. Extensible yet meaningful notation. Proof assistant users often face the need of creating new mathematical notation in order to ease the use of new concepts. The framework used in Matita for dealing with extensible notation both accounts for high quality bidimensional rendering of formulae (with the expressivity of MathMLPresentation) and provides meaningful notation, where presentational fragments are kept synchronized with semantic representation of terms. Using our approach interoperability with other systems can be achieved at the content level, and direct manipulation of formulae acting on their rendered forms is possible too. Publish/subscribe hints. Automation plays an important role in interactive proving as users like to delegate tedious proving sub-tasks to decision procedures or external reasoners. Exploiting the Web-friendliness of Matita we experimented with a broker and a network of web services (called tutors) which can try independently to complete open sub-goals of a proof, currently being authored in Matita. The user receives hints from the tutors on how to complete sub-goals and can interactively or automatically apply them to the current proof. Another innovative aspect of Matita, only marginally touched by this thesis, is the embedded content-based search engine Whelp which is exploited to various ends, from automatic theorem proving to avoiding duplicate work for the user. We also discuss the (potential) reusability in other systems of the widgets presented in this thesis and how we envisage the evolution of user interfaces for interactive theorem provers in the Web 2.0 era.

A Semantic-based Framework for Digital Survey of Architectural Heritage

The research aims at developing a framework for semantic-based digital survey of architectural heritage. Rooted in knowledge-based modeling which extracts mathematical constraints of geometry from architectural treatises, as-built information of architecture obtained from image-based modeling is integrated with the ideal model in BIM platform. The knowledge-based modeling transforms the geometry and parametric relation of architectural components from 2D printings to 3D digital models, and create large amount variations based on shape grammar in real time thanks to parametric modeling. It also provides prior knowledge for semantically segmenting unorganized survey data. The emergence of SfM (Structure from Motion) provides access to reconstruct large complex architectural scenes with high flexibility, low cost and full automation, but low reliability of metric accuracy. We solve this problem by combing photogrammetric approaches which consists of camera configuration, image enhancement, and bundle adjustment, etc. Experiments show the accuracy of image-based modeling following our workflow is comparable to that from range-based modeling. We also demonstrate positive results of our optimized approach in digital reconstruction of portico where low-texture-vault and dramatical transition of illumination bring huge difficulties in the workflow without optimization. Once the as-built model is obtained, it is integrated with the ideal model in BIM platform which allows multiple data enrichment. In spite of its promising prospect in AEC industry, BIM is developed with limited consideration of reverse-engineering from survey data. Besides representing the architectural heritage in parallel ways (ideal model and as-built model) and comparing their difference, we concern how to create as-built model in BIM software which is still an open area to be addressed. The research is supposed to be fundamental for research of architectural history, documentation and conservation of architectural heritage, and renovation of existing buildings.

A Web GIS Decision Support System For Coastal Risk Assessment and Mitigation Planning

Coastal flooding poses serious threats to coastal areas around the world, billions of dollars in damage to property and infrastructure, and threatens the lives of millions of people. Therefore, disaster management and risk assessment aims at detecting vulnerability and capacities in order to reduce coastal flood disaster risk. In particular, non-specialized researchers, emergency management personnel, and land use planners require an accurate, inexpensive method to determine and map risk associated with storm surge events and long-term sea level rise associated with climate change. This study contributes to the spatially evaluation and mapping of social-economic-environmental vulnerability and risk at sub-national scale through the development of appropriate tools and methods successfully embedded in a Web-GIS Decision Support System. A new set of raster-based models were studied and developed in order to be easily implemented in the Web-GIS framework with the purpose to quickly assess and map flood hazards characteristics, damage and vulnerability in a Multi-criteria approach. The Web-GIS DSS is developed recurring to open source software and programming language and its main peculiarity is to be available and usable by coastal managers and land use planners without requiring high scientific background in hydraulic engineering. The effectiveness of the system in the coastal risk assessment is evaluated trough its application to a real case study.

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.

Sviluppo di un framework per l'automazione dei test al banco e la prototipazione di algoritmi di controllo di motori a combustione interna

Negli ultimi anni, i limiti sempre più stringenti sulle emissioni inquinanti dei gas di scarico, hanno portato ad un notevole aumento della complessità dei motori a combustione interna. Questa complicazione determina un aumento esponenziale del numero di test da effettuare nella sala prova. I metodi tipici di gestione dei test non possono più essere utilizzati, ma è essenziale creare un sistema che ottimizzi le prove. Per ridurre drasticamente il tempo di esecuzione, è necessario implementare un'architettura in grado di facilitare lo scambio di dati tra i sistemi presenti nella sala prova, e, in aggiunta, definire le strategie di automazione dei test. L'approccio a taluni metodi si presenta ancora complicato in molti gruppi di sviluppo di strategie di controllo motore, anche se, una volta sviluppati, portano e a grandi benefici durante la fase di test. Il lavoro illustra i metodi implementati per la gestione di queste strategie. Prima si descrive l'approccio utilizzato nella calibrazione di anticipo di accensione per mantenere livelli accettabili di detonazione durante il processo di calibrazione. Successivamente è mostrato il sistema di automazione dei test che consente il pieno controllo del punto di funzionamento del motore, la gestione dell'acquisizione e la verifica della stabilità delle condizioni ottenute. L'ultima parte mostra sistemi di prototipazione rapida per la gestione di componenti innovatici del motore.

Towards a full cosmological exploitation of cosmic voids

A stately fraction of the Universe volume is dominated by almost empty space. Alongside the luminous filamentary structures that make it up, there are vast and smooth regions that have remained outside the Cosmology spotlight during the past decades: cosmic voids. Although essentially devoid of matter, voids enclose fundamental information about the cosmological framework and have gradually become an effective and competitive cosmological probe. In this Thesis work we present fundamental results about the cosmological exploitation of voids. We focused on the number density of voids as a function of their radius, known as void size function, developing an effective pipeline for its cosmological usage. We proposed a new parametrisation of the most used theoretical void size function to model voids identified in the distribution of biased tracers (i.e. dark matter haloes, galaxies and galaxy clusters), a step of fundamental importance to extend the analysis to real data surveys. We then applied our built methodology to study voids in alternative cosmological scenarios. Firstly we exploited voids with the aim of breaking the degeneracies between cosmological scenarios characterised by modified gravity and the inclusion of massive neutrinos. Secondly we analysed voids in the perspective of the Euclid survey, focusing on the void abundance constraining power on dynamical dark energy models with massive neutrinos. Moreover we explored other void statistics like void profiles and clustering (i.e. the void-galaxy and the void-void correlation), providing cosmological forecasts for the Euclid mission. We finally focused on the probe combination, highlighting the incredible potential of the joint analysis of multiple void statistics and of the combination of the void size function with different cosmological probes. Our results show the fundamental role of the void analysis in constraining the fundamental parameters of the cosmological model and pave the way for future studies on this topic.

L'applicazione del principio di autonomia come parametro di compatibilita con il diritto UE

La tesi indaga l’applicazione del principio di autonomia del diritto UE nella giurisprudenza della Corte di giustizia. In particolare, il lavoro mira ad analizzare le modalità attraverso cui il principio viene adoperato come parametro di compatibilità, ai fini dello scrutinio della Corte, in quei casi riguardanti il rapporto tra giurisdizioni di diritto internazionale e diritto dell’Unione. Una volta delineato il contesto teorico di partenza, concernente il significato dell’autonomia del diritto UE all’interno del “quadro costituzionale” dell’Unione, si passa all’analisi, caso per caso, della prassi giurisprudenziale, al fine di individuare ed estrapolare gli elementi costanti nei casi. La disamina svolta parte da pronunce celebri, tra cui il parere 1/91, Kadi e il parere 2/13, in cui il principio nasce e si sviluppa. Successivamente, si passa alle pronunce più recenti, componenti la c.d. saga Achmea, riguardante la compatibilità con il principio di autonomia dei meccanismi ISDS. I risultati raccolti nell’analisi vengono sintetizzati in modo da ricostruire un test di compatibilità unitario e astratto, composto da tre elementi. Si arriva così, per via induttiva, all’elaborazione di un modello idoneo a spiegare le modalità di applicazione del principio di autonomia come parametro di compatibilità. Sulla scorta di ciò vengono formulate considerazioni e riflessioni concernenti le principali implicazioni per l’ordinamento UE e per i suoi attori, che derivano dal principio di autonomia e dal suo utilizzo giurisprudenziale. Infine, si prende in considerazione una visione del principio di autonomia alternativa a quella emersa nel corso della trattazione e se ne valuta il potenziale impatto sulla concezione e sull’applicazione del principio stesso.

L'iniziativa dei cittadini europei: un'analisi della sua efficacia come strumento di democrazia partecipativa

Fin dalla sua attuazione nel 2012, l'Iniziativa dei cittadini europei (ICE) ha catturato l'attenzione di accademici e politici per il suo apparente potenziale come strumento di democrazia partecipativa in grado di promuovere il coinvolgimento diretto dei cittadini nel processo decisionale dell'UE. Tuttavia, dopo il suo lancio, questo strumento sembra aver deluso le speranze e le aspettative riposte in esso e, invece di fungere da ponte tra i cittadini e le istituzioni dell'UE, sembra essere diventato una chiara prova della leadership burocratica dell'UE a Bruxelles. Con la riforma della sua legislazione di attuazione, le istituzioni europee hanno voluto dare all'ICE un'altra possibilità di raggiungere il suo pieno potenziale di democratizzazione. A tre anni dall'entrata in vigore del nuovo Regolamento 2019/788 e a più di dieci anni dal suo inserimento nell'ordinamento giuridico europeo, riteniamo che sia il momento giusto per valutare il reale impatto dell'ICE nella promozione della democrazia partecipativa nell'UE. Per raggiungere questo obiettivo, la presente tesi di dottorato intraprende un'analisi completa di questa struttura di opportunità per la partecipazione dei cittadini, esplorando le sue origini, il suo quadro normativo, la sua applicazione pratica e le sue implicazioni per la democrazia europea attraverso un approccio interdisciplinare che combina l'uso di metodi sia qualitativi che quantitativi. Questa ricerca mira a fornire una comprensione più profonda e critica dell'ICE e del suo ruolo nella costruzione di un'Europa più partecipativa e più vicina ai cittadini.