On the relation among answer set solvers

In this paper, we study the relation among Answer Set Programming (ASP) systems from a computational point of view. We consider smodels, dlv, and cmodels ASP systems based on stable model semantics, the first two being native ASP systems and the last being a SAT-based system. We first show that smodels, dlv, and cmodels explore search trees with the same branching nodes (assuming, of course, a same branching heuristic) on the class of tight logic programs. Leveraging on the fact that SAT-based systems rely on the deeply studied Davis–Logemann–Loveland (dll) algorithm, we derive new complexity results for the ASP procedures. We also show that on nontight programs the SAT-based systems are computationally different from native procedures, and the latter have computational advantages. Moreover, we show that native procedures can guarantee the “correctness” of a reported solution when reaching the leaves of the search trees (i.e., no stability check is needed), while this is not the case for SAT-based procedures on nontight programs. A similar advantage holds for dlv in comparison with smodels if the “well-founded” operator is disabled and only Fitting’s operator is used for negative inferences. We finally study the “cost” of achieving such advantages and comment on to what extent the results presented extend to other systems.     

Evaluating ASP and Commercial Solvers on the CSPLib

This paper deals with four solvers for combinatorial problems: the commercial state-of-the-art solver ILOG oplstudio, and the research answer set programming (ASP) systems dlv, smodels and cmodels. The first goal of this research is to evaluate the relative performance of such systems when used in a purely declarative way, using a reproducible and extensible experimental methodology. In particular, we consider a third-party problem library, i.e., the CSPLib, and uniform rules for modelling and instance selection. The second goal is to analyze the marginal effects of popular reformulation techniques on the various solving technologies. In particular, we consider structural symmetry breaking, the adoption of global constraints, and the addition of auxiliary predicates. Finally, we evaluate, on a subset of the problems, the impact of numbers and arithmetic constraints on the different solving technologies. Results show that there is not a single solver winning on all problems, and that reformulation is almost always beneficial: symmetry-breaking may be a good choice, but its complexity has to be carefully chosen, by taking into account also the particular solver used. Global constraints often, but not always, help opl, and the addition of auxiliary predicates is usually worth, especially when dealing with ASP solvers. Moreover, interesting synergies among the various modelling techniques exist.     

Are our homes ready for services? A domotic infrastructure based on the Web service stack

The increase in computational power and the networking abilities of home appliances are revolutionizing the way we interact with our homes. This trend is growing stronger and opening a number of technological challenges. From the point of view of distributed systems, there is a need to design architectures for enhancing the comfort and safety of the home, which deals with issues of heterogeneity, scalability and openness. By considering the evolution of domotic research and projects, we advocate a role for Web services in the domestic network. We ground our claim by proposing a concrete architecture for a home in which the health of an elder is monitored. The architecture is implemented on a heterogeneous set of devices, which allows us to evaluate it and draw conclusions on the feasibility of using service-oriented approaches in ubiquitous computing.     

P2P multicast for pervasive ad hoc networks

During the last few years, the proliferation of miniaturised devices with networking capabilities has provided the technological grounds for pervasive networking environments. It is not visionary to foresee a world of pervasive devices embedded in the environment interacting between them, and with those carried by users, via wireless communications. In addition, fostered by the diffusion of small-size, computational-rich mobile devices, the way content is generated, and accessed is changing with respect to the legacy-Internet paradigm. An ever-increasing share of the Internet content is generated directly by the users, and shared on the network (following the User-Generated Content model). While today the legacy Internet is still used to share user-generated content, it is reasonable to envision that pervasive networking technologies will represent the natural platform to support this new model. This will result in content being distributed on users’ devices rather than on centralised servers on the Internet, and in users creating ad hoc networks to share content. The p2p paradigm is particularly suitable for this scenario, because communications will occur directly among users, instead of being necessarily mediated by centralised servers. Motivated by these remarks, in this work we focus on p2p multicast services over ad hoc networks aimed at sharing content among groups of users interested in the same topics. Specifically, starting from a reference solution in legacy wired networks (Scribe), we design a cross-layer optimised protocol (XScribe) that addresses most of the Scribe problems on ad hoc networks. XScribe exploits cross-layer interactions with a proactive routing protocol to manage group membership. Furthermore, it uses a lightweight, structureless approach to deliver data to group members. By jointly using experimental results and analytical models, we show that, with respect to Scribe, XScribe significantly reduces the packet loss and the delay experienced by multicast receivers, and increases the maximum throughput that can be delivered to multicast groups.     

Atomic force microscopy of protein films and crystals

A customized atomic force microscopy (AFM) instrument optimized for imaging protein crystals in solution is described. The device was tested on crystals and Langmuir-Blodgett (LB) films of two proteins with quite different molecular weights. This approach enables the periodicity and morphology of crystals to be studied in their mother liquid, thereby preserving the native periodic protein crystal structure, which is typically destroyed by drying. Moreover, the instrument appears to distinguish protein crystals from salt crystals, which under the optical microscope are frequently quite similar, the difference between them often being revealed only during x-ray analysis. AFM estimates of the packing, order, and morphology of the given single proteins appear quite similar in the LB thin film and in the crystals, which means that routine crystal measurements can be performed at high resolution. The AFM consists of a custom-built measuring head and a homemade flexible SPM controller which can drive the head for contact, noncontact and spectroscopy modes, thus providing the user with a high degree of customization for crystal measurement.     

An efficient deconvolution algorithm for estimating oxygen consumption during muscle activities

The reconstruction of an unknown input function from noisy measurements in a biological system is an ill-posed inverse problem. Any computational algorithm for its solution must use some kind of regularization technique to neutralize the disastrous effects of amplified noise components on the computed solution. In this paper, following a hierarchical Bayesian statistical inversion approach, we seek estimates for the input function and regularization parameter (hyperparameter) that maximize the posterior probability density function. We solve the maximization problem simultaneously for all unknowns, hyperparameter included, by a suitably chosen quasi-Newton method. The optimization approach is compared to the sampling-based Bayesian approach. We demonstrate the efficiency and robustness of the deconvolution algorithm by applying it to reconstructing the time courses of mitochondrial oxygen consumption during muscle state transitions (e.g., from resting state to contraction and recovery), from the simulated noisy output of oxygen concentration dynamics on the muscle surface. The model of oxygen transport and metabolism in skeletal muscle assumes an in vitro cylindrical structure of the muscle in which the oxygen from the surrounding oxygenated solution diffuses into the muscle and is then consumed by the muscle mitochondria. The algorithm can be applied to other deconvolution problems by suitably replacing the forward model of the system.     

The multimod application framework: a rapid application development tool for computer aided medicine

This paper describes a new application framework (OpenMAF) for rapid development of multimodal applications in computer-aided medicine. MAF applications are multimodal in data, in representation, and in interaction. The framework supports almost any type of biomedical data, including DICOM datasets, motion-capture recordings, or data from computer simulations (e.g. finite element modeling). The interactive visualization approach (multimodal display) helps the user interpret complex datasets, providing multiple representations of the same data. In addition, the framework allows multimodal interaction by supporting the simultaneous use of different input-output devices like 3D trackers, stereoscopic displays, haptics hardware and speech recognition/synthesis systems. The Framework has been designed to run smoothly even on limited power computers, but it can take advantage of all hardware capabilities. The Framework is based on a collection of portable libraries and it can be compiled on any platform that supports OpenGL, including Windows, MacOS X and any flavor of Unix/linux.     

Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes.     

Subacute proteome changes following traumatic injury of the developing brain: Implications for a dysregulation of neuronal migration and neurite arborization

Traumatic brain injury (TBI) is a major cause of morbidity and mortality among children and adolescents. To gain insight into developmental events influenced by TBI, we analyzed subacute mouse brain proteome changes in a percussion head trauma model at P7 ipsi- and contralateral to the site of injury. The comparison of brain proteomes of trauma mice and controls revealed reproducible changes in the intensity of 28 proteins (30 protein spots) in response to trauma. The changes detected suggest that TBI leads to apoptosis, inflammation, and oxidative stress. These changes were consistent with our results of histological and biochemical evaluation of the brains which revealed widespread apoptotic neurodegeneration, microglia activation, and increased levels of protein carbonyls. Furthermore, we detected changes in proteins involved in neuronal migration as well as axonal and dendritic growth and guidance, suggesting interference of trauma with these developmental events.     

A web-based e-learning system for increasing study efficiency by stimulating learner’s motivation

Due to the opportunities provided by the Internet, more and more people are taking advantage of distance learning courses and during the last few years enormous research efforts have been dedicated to the development of distance learning systems. So far, many e-learning systems are proposed and used practically. However, in these systems the e-learning completion rate is about 30%. One of the reasons is the low study desire when the learner studies the learning materials. In this research, we propose an interactive Web-based e-learning system. The purpose of our system is to increase the e-learning completion rate by stimulating learner’s motivation. The proposed system has three subsystems: the learning subsystem, learner support subsystem, and teacher support subsystem. The learning subsystem improves the learner’s study desire. The learner support subsystem supports the learner during the study, and the teacher support subsystem supports the teacher to get the learner’s study state. To evaluate the proposed system, we developed several experiments and surveys. By using new features such as: display of learner’s study history, change of interface color, encourage function, ranking function, self-determination of the study materials, and grouping of learners, the proposed system can increase the learning efficiency.