Logic based methods for SNPs tagging and reconstruction

SNPs are positions of the DNA sequences where the differences among individuals are embedded. The knowledge of such SNPs is crucial for disease association studies, but even if the number of such positions is low (about 1% of the entire sequence), the cost to extract the complete information is actually very high. Recent studies have shown that DNA sequences are structured into blocks of positions, that are conserved during evolution, where there is strong correlation among values (alleles) of different loci. To reduce the cost of extracting SNPs information, the block structure of the DNA has suggested to limit the process to a subset of SNPs, the so-called Tag SNPs, that are able to maintain the most of the information contained in the whole sequence. In this paper, we apply a technique for feature selection based on integer programming to the problem of Tag SNP selection. Moreover, to test the quality of our approach, we consider also the problem of SNPs reconstruction, i.e. the problem of deriving unknown SNPs from the value of Tag SNPs and propose two reconstruction methods, one based on a majority vote and the other on a machine learning approach. We test our algorithm on two public data sets of different nature, providing results that are, when comparable, in line with the related literature. One of the interesting aspects of the proposed method is to be found in its capability to deal simultaneously with very large SNPs sets, and, in addition, to provide highly informative reconstruction rules in the form of logic formulas.     

Matrix-Based Discrete Event Control for Surveillance Mobile Robotics

This paper focuses on the control system for an autonomous robot for the surveillance of indoor environments. Our approach proposes a matrix-based formalism which allows us to merge in a single framework discrete-event supervisory control, conflict resolution and reactive control. As a consequence, the robot is able to autonomously handle high level tasks as well as low-level behaviors, solving control and decision-making issues simultaneously. Moreover, the matrix-based controller is modular and can be easily reconfigured if mission characteristics or robot hardware configuration change. An illustrative example and a report on experimental investigations are provided to illustrate the main features of the proposed approach.     

An Efficient Solution for Model Checking Graph Transformation Systems

This paper presents an efficient solution for modeling checking graph transformation systems. The approach transforms AGG specifications into Bogor models and supports both attributed typed graphs and layered transformations. Resulting models are amenable to check interesting properties expressed as combinations of LTL (Linear Temporal Logic) and graph transformation rules. The first experimental results are encouraging and show that in most cases our proposal improves existing approaches, both in terms of performance and expressiveness.     

Utilizing endoscopic technology to reveal real-time proteomic alterations in response to chemoprevention

Cancer chemoprevention approaches use either pharmacological or dietary agents to impede, arrest or reverse the carcinogenic process. Although several agents have shown effectiveness against colon cancer, present intervention strategies provide only partial reduction. In this study, we utilized high-resolution endoscopy to obtain colon tumor biopsy specimens from Apc mutant mice before and after 2-wk sulindac intervention. To acquire information beyond genomics, proteome analysis using the ProteomeLab PF2D platform was implemented to generate 2-D protein expression maps from biopsies. Chromatograms produced common signature profiles between sulindac and nonsulindac treated samples, and contrasting profiles termed "fingerprints". We selected a double peak that appeared in tumor biopsies from sulindac-treated mice. Further analyses using MS sequencing identified this protein as histone H2B. The location of H2B in the 1(st) dimension strongly suggested PTM, consistent with identification of two oxidized methionines. While further studies on sulindac proteomic fingerprints are underway, this study demonstrates the feasibility and advantages of "real-time" proteomic analysis for obtaining information on biomarker discovery and drug activity that would not be revealed by a genetic assay. This approach should be broadly applicable for assessing lesion responsiveness in a wide range of translational and human clinical studies.     

Self-adaptation in next-generation Internet networks: how to react to traffic changes while respecting QoS?

Next-generation network infrastructure should support different services and several levels of quality of service (QoS) and resilience. The main requirements for such multiservice networks are flexibility, effective utilization of network resources, and ability to react to traffic demand changes with time. These requisites lead to the fact that next-generation networks should, to some extend, be "self-adapting," to cope with the need of promptly reacting to traffic demand changes, in an effective way, while taking into account the different requirements in terms of QoS. This paper sketches the reference network scenario and discusses the subject of self-adapting networks, attempting to focus on the key issues that need to be solved to realize future infrastructures. As a relevant example, this paper briefly reports a system developed by the authors' laboratory that implements a traffic engineering solution able to fulfill the mentioned requirements. This system could be regarded as a first concrete step toward the realization of self-adapting networks. In addition, some relevant results that were obtained either by simulation or by experiments on a real test bed are reported to discuss the main characteristics of such a system and assess the feasibility of the concept. Finally, the paper reviews the main hot issues that need to be addressed, in the authors' opinion, by the international research community.     

Monitoring and improving Greek banking services using Bayesian Networks: An analysis of mystery shopping data

Mystery shopping is a well known marketing technique used by companies and marketing analysts to measure quality of service, and gather information about products and services. In this article, we analyse data from mystery shopping surveys via Bayesian Networks in order to examine and evaluate the quality of service offered by the loan departments of Greek Banks. We use mystery shopping visits to collect information about loan products and services and, by this way, evaluate the customer satisfaction and plan improvement strategies that will assist banks to reach their internal standards. Bayesian Networks not only provide a pictorial representation of the dependence structure between the characteristics of interest but also allow to evaluate, interpret and understand the effects of possible improvement strategies.     

Cooperation and Competition in ALIAS: A Logic Framework for Agents that Negotiate

This paper presents ALIAS, an agent architecture based on intelligent logic agents, where the main form of agent reasoning is abduction. The system is particularly suited for solving problems where knowledge is incomplete, where agents may need to make reasonable hypotheses about the problem domain and other agents, and where the raised hypotheses have to be consistent for the overall set of agents. ALIAS agents are pro-active, exhibiting a goal-directed behavior, and autonomous, since each one can solve problems using its own private knowledge base. ALIAS agents are also social, because they are able to interact with other agents, in order to cooperatively solve problems. The coordination mechanisms are modeled by means of LAILA, a logic-based language which allows to express intra-agent reasoning and inter-agent coordination. As an application, we show how LAILA can be used to implement inter-agent dialogues, e.g., for negotiation. In particular, LAILA is well-suited to coordinate the process of negotiation aimed at exchanging resources between agents, thus allowing them to execute the plans to achieve their goals.     

Specification and Verification of Agent Interaction using Social Integrity Constraints

In this paper we propose a logic-based social approach to the specification and verification of agent interaction. We firstly introduce integrity constraints about social acts (called Social Integrity Constraints) as a formalism to express interaction protocols and to give a social semantics to the behavior of agents, focusing on communicative acts. Then, we discuss several possible kinds of verification of agent interaction, and we show how social integrity constraints can be used to verify some properties in this respect. We focus our attention on static verification of compliance of agent specifications to interaction protocols, and on run-time verification, based on agents' observable behavior. We adopt as a running example the NetBill security transaction protocol for the selling and delivery of information goods.