Specification, execution and verification of interaction protocols: an approach based on computational logic

Interaction protocols establish how different computational entities can interact with each other. The interaction can be finalized to the exchange of data, as in 'communication protocols', or can be oriented to achieve some result, as in 'application protocols'. Moreover, with the increasing complexity of modern distributed systems, protocols are used also to control such a complexity, and to ensure that the system as a whole evolves with certain features. However, the extensive use of protocols has raised some issues, from the language for specifying them to the several verification aspects. Computational Logic provides models, languages and tools that can be effectively adopted to address such issues: its declarative nature can be exploited for a protocol specification language, while its operational counterpart can be used to reason upon such specifications. In this thesis we propose a proof-theoretic framework, called SCIFF, together with its extensions. SCIFF is based on Abductive Logic Programming, and provides a formal specification language with a clear declarative semantics (based on abduction). The operational counterpart is given by a proof procedure, that allows to reason upon the specifications and to test the conformance of given interactions w.r.t. a defined protocol. Moreover, by suitably adapting the SCIFF Framework, we propose solutions for addressing (1) the protocol properties verification (g-SCIFF Framework), and (2) the a-priori conformance verification of peers w.r.t. the given protocol (AlLoWS Framework). We introduce also an agent based architecture, the SCIFF Agent Platform, where the same protocol specification can be used to program and to ease the implementation task of the interacting peers.

Specification and Verification of Declarative Open Interaction Models - A Logic-based framework

The advent of distributed and heterogeneous systems has laid the foundation for the birth of new architectural paradigms, in which many separated and autonomous entities collaborate and interact to the aim of achieving complex strategic goals, impossible to be accomplished on their own. A non exhaustive list of systems targeted by such paradigms includes Business Process Management, Clinical Guidelines and Careflow Protocols, Service-Oriented and Multi-Agent Systems. It is largely recognized that engineering these systems requires novel modeling techniques. In particular, many authors are claiming that an open, declarative perspective is needed to complement the closed, procedural nature of the state of the art specification languages. For example, the ConDec language has been recently proposed to target the declarative and open specification of Business Processes, overcoming the over-specification and over-constraining issues of classical procedural approaches. On the one hand, the success of such novel modeling languages strongly depends on their usability by non-IT savvy: they must provide an appealing, intuitive graphical front-end. On the other hand, they must be prone to verification, in order to guarantee the trustworthiness and reliability of the developed model, as well as to ensure that the actual executions of the system effectively comply with it. In this dissertation, we claim that Computational Logic is a suitable framework for dealing with the specification, verification, execution, monitoring and analysis of these systems. We propose to adopt an extended version of the ConDec language for specifying interaction models with a declarative, open flavor. We show how all the (extended) ConDec constructs can be automatically translated to the CLIMB Computational Logic-based language, and illustrate how its corresponding reasoning techniques can be successfully exploited to provide support and verification capabilities along the whole life cycle of the targeted systems.

Comparative genomic sequencing analysis of a region in human chromosome 11p15.3, mouse chromosome 7 and analysis of the novel STK33, Stk33 gene

The comparative genomic sequence analysis of a region in human chromosome 11p15.3 and its homologous segment in mouse chromosome 7 between ST5 and LMO1 genes has been performed. 158,201 bases were sequenced in the mouse and compared with the syntenic region in human, partially available in the public databases. The analysed region exhibits the typical eukaryotic genomic structure and compared with the close neighbouring regions, strikingly reflexes the mosaic pattern distribution of (G+C) and repeats content despites its relative short size. Within this region the novel gene STK33 was discovered (Stk33 in the mouse), that codes for a serine/threonine kinase. The finding of this gene constitutes an excellent example of the strength of the comparative sequencing approach. Poor gene-predictions in the mouse genomic sequence were corrected and improved by the comparison with the unordered data from the human genomic sequence publicly available. Phylogenetical analysis suggests that STK33 belongs to the calcium/calmodulin-dependent protein kinases group and seems to be a novelty in the chordate lineage. The gene, as a whole, seems to evolve under purifying selection whereas some regions appear to be under strong positive selection. Both human and mouse versions of serine/threonine kinase 33, consists of seventeen exons highly conserved in the coding regions, particularly in those coding for the core protein kinase domain. Also the exon/intron structure in the coding regions of the gene is conserved between human and mouse. The existence and functionality of the gene is supported by the presence of entries in the EST databases and was in vivo fully confirmed by isolating specific transcripts from human uterus total RNA and from several mouse tissues. Strong evidence for alternative splicing was found, which may result in tissue-specific starting points of transcription and in some extent, different protein N-termini. RT-PCR and hybridisation experiments suggest that STK33/Stk33 is differentially expressed in a few tissues and in relative low levels. STK33 has been shown to be reproducibly down-regulated in tumor tissues, particularly in ovarian tumors. RNA in-situ hybridisation experiments using mouse Stk33-specific probes showed expression in dividing cells from lung and germinal epithelium and possibly also in macrophages from kidney and lungs. Preliminary experimentation with antibodies designed in this work, performed in parallel to the preparation of this manuscript, seems to confirm this expression pattern. The fact that the chromosomal region 11p15 in which STK33 is located may be associated with several human diseases including tumor development, suggest further investigation is necessary to establish the role of STK33 in human health.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Characterization and optimization of an x-ray laser for the spectroscopy of Li-like heavy-ions

Recent developments in the theory of plasma-based collisionally excited x-ray lasers (XRL) have shown an optimization potential based on the dependence of the absorption region of the pumping laser on its angle of incidence on the plasma. For the experimental proof of this idea, a number of diagnostic schemes were developed, tested, qualified and applied. A high-resolution imaging system, yielding the keV emission profile perpendicular to the target surface, provided positions of the hottest plasma regions, interesting for the benchmarking of plasma simulation codes. The implementation of a highly efficient spectrometer for the plasma emission made it possible to gain information about the abundance of the ionization states necessary for the laser action in the plasma. The intensity distribution and deflection angle of the pump laser beam could be imaged for single XRL shots, giving access to its refraction process within the plasma. During a European collaboration campaign at the Lund Laser Center, Sweden, the optimization of the pumping laser incidence angle resulted in a reduction of the required pumping energy for a Ni-like Mo XRL, which enabled the operation at a repetition rate of 10 Hz. Using the experiences gained there, the XRL performance at the PHELIX facility, GSI Darmstadt with respect to achievable repetition rate and at wavelengths below 20 nm was significantly improved, and also important information for the development towards multi-100 eV plasma XRLs was acquired. Due to the setup improvements achieved during the work for this thesis, the PHELIX XRL system now has reached a degree of reproducibility and versatility which is sufficient for demanding applications like the XRL spectroscopy of heavy ions. In addition, a European research campaign, aiming towards plasma XRLs approaching the water-window (wavelengths below 5 nm) was initiated.

The language of others mirrored in thy face: The role of political affiliation in automatic facial effects of language

People tend to automatically mimic facial expressions of others. If clear evidence exists on the effect of non-verbal behavior (emotion faces) on automatic facial mimicry, little is known about the role of verbal behavior (emotion language) in triggering such effects. Whereas it is well-established that political affiliation modulates facial mimicry, no evidence exists on whether this modulation passes also through verbal means. This research addressed the role of verbal behavior in triggering automatic facial effects depending on whether verbal stimuli are attributed to leaders of different political parties. Study 1 investigated the role of interpersonal verbs, referring to positive and negative emotion expressions and encoding them at different levels of abstraction, in triggering corresponding facial muscle activation in a reader. Study 2 examined the role of verbs expressing positive and negative emotional behaviors of political leaders in modulating automatic facial effects depending on the matched or mismatched political affiliation of participants and politicians of left-and right-wing. Study 3 examined whether verbs expressing happiness displays of ingroup politicians induce a more sincere smile (Duchenne) pattern among readers of same political affiliation relative to happiness expressions of outgroup politicians. Results showed that verbs encoding facial actions at different levels of abstraction elicited differential facial muscle activity (Study 1). Furthermore, political affiliation significantly modulated facial activation triggered by emotion verbs as participants showed more congruent and enhanced facial activity towards ingroup politicians’ smiles and frowns compared to those of outgroup politicians (Study 2). Participants facially responded with a more sincere smile pattern towards verbs expressing smiles of ingroup compared to outgroup politicians (Study 3). Altogether, results showed that the role of political affiliation in modulating automatic facial effects passes also through verbal channels and is revealed at a fine-grained level by inducing quantitative and qualitative differences in automatic facial reactions of readers.

Regional origin and decrease of pain in patients with depressive symptoms under treatment with venlafaxine

Patient's language, tradition, conventions, and customs may all determine integration into a society and are also part of the doctor-patient relationship that influences diagnostic and therapeutic outcome. Language barrier and sociocultural disparity of Eastern and Southern European patients may hamper recovery from pain and depression compared to Middle European patients in Switzerland.

"Framing Counterspaces: Forms and Meanings of Graffiti in Berlin's Linguistic Landscape"

Street art and graffiti are integral parts of Berlin’s urban space, which has undergone dramatic transformations in the past two decades. Graffiti texts constitute a critical comment on these urban transformations. This talk analyzes the connection between the phenomenon of street art and trajectories in urban planning in post-wall Berlin. My current research explores the meaning of various forms of street art (such as graffiti, posters, sticker art, stencils) as texts in Berlin’s linguistic landscape. Linguistic Landscape research pays critical attention to language, words, and images displayed and exposed in public spaces. The field of Linguistic Landscapes has only recently begun to include graffiti texts in analyses of text and space to fully comprehend the semiotics of the street. In the case of Germany’s capital, graffiti writing enters into a critical dialogue with the environment and provides a readable text to understand the city.

The Semantics and Typology of Yes/No Particles (A Cross-Linguistic Study)

Taking the three basic systems of Yes/No particles the group looked at the relative deep and surface structures, and asked what types of systems are present in the Georgian, Polish and Armenian languages. The choice of languages was of particular interest as the Caucasian and Indo-European languages usually have different question-answering systems, but Georgian (Caucasian) and Polish (Indo-European) in fact share the same system. The Armenian language is Indo-European, but the country is situated in the southern Caucasus, on Georgia's southern border, making it worth analysing Armenian in comparison with Georgian (from the point of view of language interference) and with Polish (as two relative languages). The group identified two different deep structures, tracing the occurrence of these in different languages, and showed that one is more natural in the majority of languages. They found no correspondence between relative languages and their question-answer systems and demonstrated that languages in the same typological class may show different systems, as with Georgian and the North Caucasian languages. It became clear that Georgian, Armenian and Polish all have an agree/disagree question-answering system defined by the same deep structure. From this they conclude that the lingual mentalities of Georgians, Armenians and Poles are more oriented to the communicative act. At the same time the Yes/No system, in which a positive particle stands for a positive answer and a negative particle for a negative answer, also functions in these languages, indicating that the second deep structure identified also functions alongside the first.

Synchronous Description of the Grammatical Structure of Modern Romani and Elaboration of Romani Textbook

The first outcome of this project was a synchronous description of the most widely spoken Romani dialect in the Czech and Slovak Republics, aimed at teachers and lecturers of the Romani language. This is intended to serve as a methodological guide for the demonstration of various grammatical phenomena, but may also assist people who want a basic knowledge of the linguistic structure of this neo-Indian language. The grammatical material is divided into 23 chapters, in a sequence which may be followed in teaching or studying. The book includes examples of the grammatical elements, but not exercises or articles. The second work produced was a textbook of Slovak Romani, which is the most detailed in the Czech or Slovak Republics to date. It is aimed at all those interested in active use of the Romani language: high school and university students, people working with the Roma, and Roma who speak little or nothing of the language of their forebears, The book includes 34 lessons, each containing relevant Romani tests (articles and dialogues), a short vocabulary list, grammatical explanations, exercises and examples of Romani written or oral expression. The textbook also contains a considerable amount of ethno-cultural information and notes on the life and traditions of the Roman, as well as pointing out some differences between different dialects. A brief Romani-Czech phrase book is included as an appendix.

Standard Language in Bosna and Hercegovina - in Language Policy Documents

From the beginning of the standardisation of language in Bosnia and Herzegovina, i.e. from the acceptance of Karadzic's phonetic spelling in the mid-19th century, to the present day when there are three different language standards in force - Bosniac (Muslim), Croatian and Serbian, language in Bosnia and Herzegovina has been a subject of political conflict. Documents on language policy from this period show the degree to which domestic and foreign political factors influenced the standard language issue, beginning with the very appellation for the specific norm regulation. The material analysed (proclamations by political, cultural and other organisations as well as corresponding constitutional and statutory provisions on language use) shows the differing treatment of the standard language in Bosnia and Herzegovina in different historical periods. During the period of Turkish rule (until 1878) there was no real political interest in the issue. Under Austro-Hungarian rule (1878-1918) there was an attempt to use the language as a means of forming a united Bosnian nation, but this was later abandoned. During the first Yugoslavia (1918-1941) a uniform solution was imposed on Bosnia and Herzegovina, as throughout the Serbo-Croatian language area, while under the Independent State of Croatia (1941-1945), the official language of Bosnia and Herzegovina was Croatian. The period from 1945 to 1991 had two phases: the first a standard language unity of Serbs, Croats, Muslims and Montenegrins (until 1965), and the second a gradual but stormy separation of national languages, which has been largely completed since 1991. The introductory study includes a detailed analysis of all the expressions used, with special reference to the present state, and accompanies the collection of documents which represent the main outcome of the research.

Discrete element methods for asphalt concrete : development and application of user-defined microstructural models and a viscoelastic micromechanical model

As an important Civil Engineering material, asphalt concrete (AC) is commonly used to build road surfaces, airports, and parking lots. With traditional laboratory tests and theoretical equations, it is a challenge to fully understand such a random composite material. Based on the discrete element method (DEM), this research seeks to develop and implement computer models as research approaches for improving understandings of AC microstructure-based mechanics. In this research, three categories of approaches were developed or employed to simulate microstructures of AC materials, namely the randomly-generated models, the idealized models, and image-based models. The image-based models were recommended for accurately predicting AC performance, while the other models were recommended as research tools to obtain deep insight into the AC microstructure-based mechanics. A viscoelastic micromechanical model was developed to capture viscoelastic interactions within the AC microstructure. Four types of constitutive models were built to address the four categories of interactions within an AC specimen. Each of the constitutive models consists of three parts which represent three different interaction behaviors: a stiffness model (force-displace relation), a bonding model (shear and tensile strengths), and a slip model (frictional property). Three techniques were developed to reduce the computational time for AC viscoelastic simulations. It was found that the computational time was significantly reduced to days or hours from years or months for typical three-dimensional models. Dynamic modulus and creep stiffness tests were simulated and methodologies were developed to determine the viscoelastic parameters. It was found that the DE models could successfully predict dynamic modulus, phase angles, and creep stiffness in a wide range of frequencies, temperatures, and time spans. Mineral aggregate morphology characteristics (sphericity, orientation, and angularity) were studied to investigate their impacts on AC creep stiffness. It was found that aggregate characteristics significantly impact creep stiffness. Pavement responses and pavement-vehicle interactions were investigated by simulating pavement sections under a rolling wheel. It was found that wheel acceleration, steadily moving, and deceleration significantly impact contact forces. Additionally, summary and recommendations were provided in the last chapter and part of computer programming codes wree provided in the appendixes.