Introducing spatial information into predictive NF-kappa B modelling - an agent-based approach

Nature is governed by local interactions among lower-level sub-units, whether at the cell, organ, organism, or colony level. Adaptive system behaviour emerges via these interactions, which integrate the activity of the sub-units. To understand the system level it is necessary to understand the underlying local interactions. Successful models of local interactions at different levels of biological organisation, including epithelial tissue and ant colonies, have demonstrated the benefits of such 'agent-based' modelling [1-4]. Here we present an agent-based approach to modelling a crucial biological system the intracellular NF-kappa B signalling pathway. The pathway is vital to immune response regulation, and is fundamental to basic survival in a range of species [5-7]. Alterations in pathway regulation underlie a variety of diseases, including atherosclerosis and arthritis. Our modelling of individual molecules, receptors and genes provides a more comprehensive outline of regulatory network mechanisms than previously possible with equation-based approaches [8]. The method also permits consideration of structural parameters in pathway regulation; here we predict that inhibition of NF-kappa B is directly affected by actin filaments of the cytoskeleton sequestering excess inhibitors, therefore regulating steady-state and feedback behaviour

Leveraging Semantic Web Service Descriptions for Validation by Automated Functional Testing

Recent years have seen the utilisation of Semantic Web Service descriptions for automating a wide range of service-related activities, with a primary focus on service discovery, composition, execution and mediation. An important area which so far has received less attention is service validation, whereby advertised services are proven to conform to required behavioural specifications. This paper proposes a method for validation of service-oriented systems through automated functional testing. The method leverages ontology-based and rule-based descriptions of service inputs, outputs, preconditions and effects (IOPE) for constructing a stateful EFSM specification. The specification is subsequently utilised for functional testing and validation using the proven Stream X-machine (SXM) testing methodology. Complete functional test sets are generated automatically at an abstract level and are then applied to concrete Web services, using test drivers created from the Web service descriptions. The testing method comes with completeness guarantees and provides a strong method for validating the behaviour of Web services

An Agent Based Approach of Collective Foraging

In this paper the behaviour of a bee colony is modeled as a society of communicating agents acting in parallel and synchroniz-ing their behaviour. Two computational models for defining the agents behaviour are introduced and compared and tools developed for these models are briefly illustrated.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Effects of exenatide twice daily versus sitagliptin on 24-h glucose, glucoregulatory and hormonal measures: a randomized, double-blind, crossover study

Aim: To compare exenatide and sitagliptin glucose and glucoregulatory measures in subjects with type 2 diabetes

Modelling of Multi-Agent Systems: Experiences with Membrane Computing and Future Challenges

Formal modelling of Multi-Agent Systems (MAS) is a challenging task due to high complexity, interaction, parallelism and continuous change of roles and organisation between agents. In this paper we record our research experience on formal modelling of MAS. We review our research throughout the last decade, by describing the problems we have encountered and the decisions we have made towards resolving them and providing solutions. Much of this work involved membrane computing and classes of P Systems, such as Tissue and Population P Systems, targeted to the modelling of MAS whose dynamic structure is a prominent characteristic. More particularly, social insects (such as colonies of ants, bees, etc.), biology inspired swarms and systems with emergent behaviour are indicative examples for which we developed formal MAS models. Here, we aim to review our work and disseminate our findings to fellow researchers who might face similar challenges and, furthermore, to discuss important issues for advancing research on the application of membrane computing in MAS modelling.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314

Model-based Testing in Cloud Brokerage Scenarios

In future Cloud ecosystems, brokers will mediate between service providers and consumers, playing an increased role in quality assurance, checking services for functional compliance to agreed standards, among other aspects. To date, most Software-as-a-Service (SaaS) testing has been performed manually, requiring duplicated effort at the development, certification and deployment stages of the service lifecycle. This paper presents a strategy for achieving automated testing for certification and re-certification of SaaS applications, based on the adoption of simple state-based and functional specifications. High-level test suites are generated from specifications, by algorithms that provide the necessary and sufficient coverage. The high-level tests must be grounded for each implementation technology, whether SOAP, REST or rich-client. Two examples of grounding are presented, one into SOAP for a traditional web service and the other into Selenium for a SAP HANA rich-client application. The results demonstrate good test coverage. Further work is required to fully automate the grounding

Culture shapes how we look at faces

Background: Face processing, amongst many basic visual skills, is thought to be invariant across all humans. From as early as 1965, studies of eye movements have consistently revealed a systematic triangular sequence of fixations over the eyes and the mouth, suggesting that faces elicit a universal, biologically-determined information extraction pattern. Methodology/Principal Findings: Here we monitored the eye movements of Western Caucasian and East Asian observers while they learned, recognized, and categorized by race Western Caucasian and East Asian faces. Western Caucasian observers reproduced a scattered triangular pattern of fixations for faces of both races and across tasks. Contrary to intuition, East Asian observers focused more on the central region of the face. Conclusions/Significance: These results demonstrate that face processing can no longer be considered as arising from a universal series of perceptual events. The strategy employed to extract visual information from faces differs across cultures

Helicobacter pylori and cancer among adults in Uganda

Data from Africa on infection with Helicobacter pylori (H. pylori) are sparse. Therefore, as part of an epidemiological study of cancer in Uganda, we investigated the prevalence and determinants of antibodies against H. pylori among 854 people with different cancer types and benign tumours. Patients were recruited from hospitals in Kampala, Uganda, interviewed about various demographic and lifestyle factors and tested for antibodies against H. pylori. In all patients combined, excluding those with stomach cancer (which has been associated with H. pylori infection), the prevalence of antibodies was 87% (723/833) overall, but declined with increasing age (p = 0.02) and was lower among people who were HIV seropositive compared to seronegative (p <0.001). Otherwise, there were few consistent epidemiological associations. Among those with stomach cancer, 18/21 (86%) had anti-H. pylori antibodies (odds ratio 0.8, 95% confidence intervals 0.2–2.9, p = 0.7; estimated using all other patients as controls, with adjustment for age, sex and HIV serostatus). No other cancer site or type was significantly associated with anti-H. pylori antibodies. The prevalence of H. pylori reported here is broadly in accord with results from other developing countries, although the determinants of infection and its' role in the aetiology of gastric cancer in Uganda remain unclear

Testing timed systems modeled by stream X-machines

Stream X-machines have been used to specify real systems where complex data structures. They are a variety of extended finite state machine where a shared memory is used to represent communications between the components of systems. In this paper we introduce an extension of the Stream X-machines formalism in order to specify systems that present temporal requirements. We add time in two different ways. First, we consider that (output) actions take time to be performed. Second, our formalism allows to specify timeouts. Timeouts represent the time a system can wait for the environment to react without changing its internal state. Since timeous affect the set of available actions of the system, a relation focusing on the functional behavior of systems, that is, the actions that they can perform, must explicitly take into account the possible timeouts. In this paper we also propose a formal testing methodology allowing to systematically test a system with respect to a specification. Finally, we introduce a test derivation algorithm. Given a specification, the derived test suite is sound and complete, that is, a system under test successfully passes the test suite if and only if this system conforms to the specification