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.

Design and Performance Evaluation of Network-on-Chip Communication Protocols and Architectures

The scale down of transistor technology allows microelectronics manufacturers such as Intel and IBM to build always more sophisticated systems on a single microchip. The classical interconnection solutions based on shared buses or direct connections between the modules of the chip are becoming obsolete as they struggle to sustain the increasing tight bandwidth and latency constraints that these systems demand. The most promising solution for the future chip interconnects are the Networks on Chip (NoC). NoCs are network composed by routers and channels used to inter- connect the different components installed on the single microchip. Examples of advanced processors based on NoC interconnects are the IBM Cell processor, composed by eight CPUs that is installed on the Sony Playstation III and the Intel Teraflops pro ject composed by 80 independent (simple) microprocessors. On chip integration is becoming popular not only in the Chip Multi Processor (CMP) research area but also in the wider and more heterogeneous world of Systems on Chip (SoC). SoC comprehend all the electronic devices that surround us such as cell-phones, smart-phones, house embedded systems, automotive systems, set-top boxes etc... SoC manufacturers such as ST Microelectronics , Samsung, Philips and also Universities such as Bologna University, M.I.T., Berkeley and more are all proposing proprietary frameworks based on NoC interconnects. These frameworks help engineers in the switch of design methodology and speed up the development of new NoC-based systems on chip. In this Thesis we propose an introduction of CMP and SoC interconnection networks. Then focusing on SoC systems we propose: • a detailed analysis based on simulation of the Spidergon NoC, a ST Microelectronics solution for SoC interconnects. The Spidergon NoC differs from many classical solutions inherited from the parallel computing world. Here we propose a detailed analysis of this NoC topology and routing algorithms. Furthermore we propose aEqualized a new routing algorithm designed to optimize the use of the resources of the network while also increasing its performance; • a methodology flow based on modified publicly available tools that combined can be used to design, model and analyze any kind of System on Chip; • a detailed analysis of a ST Microelectronics-proprietary transport-level protocol that the author of this Thesis helped developing; • a simulation-based comprehensive comparison of different network interface designs proposed by the author and the researchers at AST lab, in order to integrate shared-memory and message-passing based components on a single System on Chip; • a powerful and flexible solution to address the time closure exception issue in the design of synchronous Networks on Chip. Our solution is based on relay stations repeaters and allows to reduce the power and area demands of NoC interconnects while also reducing its buffer needs; • a solution to simplify the design of the NoC by also increasing their performance and reducing their power and area consumption. We propose to replace complex and slow virtual channel-based routers with multiple and flexible small Multi Plane ones. This solution allows us to reduce the area and power dissipation of any NoC while also increasing its performance especially when the resources are reduced. This Thesis has been written in collaboration with the Advanced System Technology laboratory in Grenoble France, and the Computer Science Department at Columbia University in the city of New York.

Study of the components of quality in SO2-free wines obtained by innovative vinification protocols. Evaluation of the pre-fermentative addition of lysozyme and oenological tannins.

The research performed during the PhD candidature was intended to evaluate the quality of white wines, as a function of the reduction in SO2 use during the first steps of the winemaking process. In order to investigate the mechanism and intensity of interactions occurring between lysozyme and the principal macro-components of musts and wines, a series of experiments on model wine solutions were undertaken, focusing attention on the polyphenols, SO2, oenological tannins, pectines, ethanol, and sugar components. In the second part of this research program, a series of conventional sulphite added vinifications were compared to vinifications in which sulphur dioxide was replaced by lysozyme and consequently define potential winemaking protocols suitable for the production of SO2-free wines. To reach the final goal, the technological performance of two selected yeast strains with a low aptitude to produce SO2 during fermentation were also evaluated. The data obtained suggested that the addition of lysozyme and oenological tannins during the alcoholic fermentation could represent a promising alternative to the use of sulphur dioxide and a reliable starting point for the production of SO2-free wines. The different vinification protocols studied influenced the composition of the volatile profile in wines at the end of the alcoholic fermentation, especially with regards to alcohols and ethyl esters also a consequence of the yeast’s response to the presence or absence of sulphites during fermentation, contributing in different ways to the sensory profiles of wines. In fact, the aminoacids analysis showed that lysozyme can affect the consumption of nitrogen as a function of the yeast strain used in fermentation. During the bottle storage, the evolution of volatile compounds is affected by the presence of SO2 and oenological tannins, confirming their positive role in scaveging oxygen and maintaining the amounts of esters over certain levels, avoiding a decline in the wine’s quality. Even though a natural decrease was found on phenolic profiles due to oxidation effects caused by the presence of oxygen dissolved in the medium during the storage period, the presence of SO2 together with tannins contrasted the decay of phenolic content at the end of the fermentation. Tannins also showed a central role in preserving the polyphenolic profile of wines during the storage period, confirming their antioxidant property, acting as reductants. Our study focused on the fundamental chemistry relevant to the oxidative phenolic spoilage of white wines has demonstrated the suitability of glutathione to inhibit the production of yellow xanthylium cation pigments generated from flavanols and glyoxylic acid at the concentration that it typically exists in wine. The ability of glutathione to bind glyoxylic acid rather than acetaldehyde may enable glutathione to be used as a ‘switch’ for glyoxylic acid-induced polymerisation mechanisms, as opposed to the equivalent acetaldehyde polymerisation, in processes such as microoxidation. Further research is required to assess the ability of glutathione to prevent xanthylium cation production during the in-situ production of glyoxylic acid and in the presence of sulphur dioxide.

Development of motion analysis protocols based on inertial sensors

The aim of this thesis was to describe the development of motion analysis protocols for applications on upper and lower limb extremities, by using inertial sensors-based systems. Inertial sensors-based systems are relatively recent. Knowledge and development of methods and algorithms for the use of such systems for clinical purposes is therefore limited if compared with stereophotogrammetry. However, their advantages in terms of low cost, portability, small size, are a valid reason to follow this direction. When developing motion analysis protocols based on inertial sensors, attention must be given to several aspects, like the accuracy of inertial sensors-based systems and their reliability. The need to develop specific algorithms/methods and software for using these systems for specific applications, is as much important as the development of motion analysis protocols based on them. For this reason, the goal of the 3-years research project described in this thesis was achieved first of all trying to correctly design the protocols based on inertial sensors, in terms of exploring and developing which features were suitable for the specific application of the protocols. The use of optoelectronic systems was necessary because they provided a gold standard and accurate measurement, which was used as a reference for the validation of the protocols based on inertial sensors. The protocols described in this thesis can be particularly helpful for rehabilitation centers in which the high cost of instrumentation or the limited working areas do not allow the use of stereophotogrammetry. Moreover, many applications requiring upper and lower limb motion analysis to be performed outside the laboratories will benefit from these protocols, for example performing gait analysis along the corridors. Out of the buildings, the condition of steady-state walking or the behavior of the prosthetic devices when encountering slopes or obstacles during walking can also be assessed. The application of inertial sensors on lower limb amputees presents conditions which are challenging for magnetometer-based systems, due to ferromagnetic material commonly adopted for the construction of idraulic components or motors. INAIL Prostheses Centre stimulated and, together with Xsens Technologies B.V. supported the development of additional methods for improving the accuracy of MTx in measuring the 3D kinematics for lower limb prostheses, with the results provided in this thesis. In the author’s opinion, this thesis and the motion analysis protocols based on inertial sensors here described, are a demonstration of how a strict collaboration between the industry, the clinical centers, the research laboratories, can improve the knowledge, exchange know-how, with the common goal to develop new application-oriented systems.

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.

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.

Mac protocols for linear wireless (sensor) networks

Wireless sensor networks (WSNs) consist of a large number of sensor nodes, characterized by low power constraint, limited transmission range and limited computational capabilities [1][2].The cost of these devices is constantly decreasing, making it possible to use a large number of sensor devices in a wide array of commercial, environmental, military, and healthcare fields. Some of these applications involve placing the sensors evenly spaced on a straight line for example in roads, bridges, tunnels, water catchments and water pipelines, city drainages, oil and gas pipelines etc., making a special class of these networks which we define as a Linear Wireless Network (LWN). In LWNs, data transmission happens hop by hop from the source to the destination, through a route composed of multiple relays. The peculiarity of the topology of LWNs, motivates the design of specialized protocols, taking advantage of the linearity of such networks, in order to increase reliability, communication efficiency, energy savings, network lifetime and to minimize the end-to-end delay [3]. In this thesis a novel contention based Medium Access Control (MAC) protocol called L-CSMA, specifically devised for LWNs is presented. The basic idea of L-CSMA is to assign different priorities to nodes based on their position along the line. The priority is assigned in terms of sensing duration, whereby nodes closer to the destination are assigned shorter sensing time compared to the rest of the nodes and hence higher priority. This mechanism speeds up the transmission of packets which are already in the path, making transmission flow more efficient. Using NS-3 simulator, the performance of L-CSMA in terms of packets success rate, that is, the percentage of packets that reach destination, and throughput are compared with that of IEEE 802.15.4 MAC protocol, de-facto standard for wireless sensor networks. In general, L-CSMA outperforms the IEEE 802.15.4 MAC protocol.

Dental arch relationship in children with complete unilateral cleft lip and palate following one-stage and three-stage surgical protocols

The objective of this study is to compare dental arch relationship following one-stage and three-stage surgical protocols of unilateral cleft lip and palate. Dental casts of 61 children (mean age, 11.2 years; SD, 1.7), consecutively treated in one center with one-stage closure of the complete cleft at 9.2 months (SD, 2.0), were compared with a sample of 97 patients (mean age, 8.7 years; SD, 0.9), consecutively treated with a three-stage protocol including delayed hard palate closure in another center. The dental casts were assigned random numbers to blind their origin. Four raters graded dental arch relationship and palatal morphology using the EUROCRAN index. The strength of agreement of rating was assessed with kappa statistics. Independent t tests were run to compare the EUROCRAN scores between one-stage and three-stage samples, and Fisher's exact tests were performed to evaluate differences of distribution of the EUROCRAN grades. The intra- and inter-rater agreement was moderate to very good. Dental arch relationship in the one-stage sample was less favorable than in three-stage group (mean scores, 2.58 and 1.97 for one-stage and three-stage samples, respectively; p?dental arch relationship following one-stage repair was less favorable than the outcome of three-stage repair. The palatal morphology following one-stage repair, however, was more favorable than the outcome of three-stage repair.

Delivery room management of very low birth weight infants in Germany, Austria and Switzerland--a comparison of protocols

Surveys from the USA, Australia and Spain have shown significant inter-institutional variation in delivery room (DR) management of very low birth weight infants (VLBWI, <1500g) at birth, despite regularly updated international guidelines.

Confocal imaging protocols for live/dead staining in three-dimensional carriers

In tissue engineering, a variety of methods are commonly used to evaluate survival of cells inside tissues or three-dimensional (3D) carriers. Among these methods confocal laser scanning microscopy opened accessibility of 3D tissue using live cell imaging into the tissue or 3D scaffolds. However, although this technique is ideally applied to 3D tissue or scaffolds with thickness up to several millimetres, this application is surprisingly rare and scans are often done on slices with thickness <20 μm. Here, we present novel protocols for the staining of 3D tissue (e.g. intervertebral disc tissue) and scaffolds, such as fibrin gels or alginate beads.

Effect of two beta-alanine dosing protocols on muscle carnosine synthesis and washout

Carnosine (β-alanyl-L-histidine) is found in high concentrations in skeletal muscle and chronic β-alanine (BA) supplementation can increase carnosine content. This placebo-controlled, double-blind study compared two different 8-week BA dosing regimens on the time course of muscle carnosine loading and 8-week washout, leading to a BA dose-response study with serial muscle carnosine assessments throughout. Thirty-one young males were randomized into three BA dosing groups: (1) high-low: 3.2 g BA/day for 4 weeks, followed by 1.6 g BA/day for 4 weeks; (2) low-low: 1.6 g BA/day for 8 weeks; and (3) placebo. Muscle carnosine in tibialis-anterior (TA) and gastrocnemius (GA) muscles was measured by 1H-MRS at weeks 0, 2, 4, 8, 12 and 16. Flushing symptoms and blood clinical chemistry were trivial in all three groups and there were no muscle carnosine changes in the placebo group. During the first 4 weeks, the increase for high-low (TA 2.04 mmol/kgww, GA 1.75 mmol/kgww) was ~twofold greater than low-low (TA 1.12 mmol/kgww, GA 0.80 mmol/kgww). 1.6 g BA/day significantly increased muscle carnosine within 2 weeks and induced continual rises in already augmented muscle carnosine stores (week 4-8, high-low regime). The dose-response showed a carnosine increase of 2.01 mmol/kgww per 100 g of consumed BA, which was only dependent upon the total accumulated BA consumed (within a daily intake range of 1.6-3.2 g BA/day). Washout rates were gradual (0.18 mmol/kgww and 0.43 mmol/kgww/week; ~2%/week). In summary, the absolute increase in muscle carnosine is only dependent upon the total BA consumed and is not dependent upon baseline muscle carnosine, the muscle type, or the daily amount of supplemented BA.