Checking experiments for stream X-machines

This article is a post-print version of the published article which may be accessed at the link below. Copyright © 2010 Elsevier B.V. All rights reserved.Stream X-machines are a state based formalism that has associated with it a particular development process in which a system is built from trusted components. Testing thus essentially checks that these components have been combined in a correct manner and that the orders in which they can occur are consistent with the specification. Importantly, there are test generation methods that return a checking experiment: a test that is guaranteed to determine correctness as long as the implementation under test (IUT) is functionally equivalent to an unknown element of a given fault domain Ψ. Previous work has show how three methods for generating checking experiments from a finite state machine (FSM) can be adapted to testing from a stream X-machine. However, there are many other methods for generating checking experiments from an FSM and these have a variety of benefits that correspond to different testing scenarios. This paper shows how any method for generating a checking experiment from an FSM can be adapted to generate a checking experiment for testing an implementation against a stream X-machine. This is the case whether we are testing to check that the IUT is functionally equivalent to a specification or we are testing to check that every trace (input/output sequence) of the IUT is also a trace of a nondeterministic specification. Interestingly, this holds even if the fault domain Ψ used is not that traditionally associated with testing from a stream X-machine. The results also apply for both deterministic and nondeterministic implementations

Morphomics predicts response to ipilimumab in patients with stage IV melanoma

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113727/1/jso24003.pd

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

Simulating heterogeneous behaviours in complex systems on GPUs

Agent Based Modelling (ABM) is an approach for modelling dynamic systems and studying complex and emergent behaviour. ABMs have been widely applied in diverse disciplines including biology, economics, and social sciences. The scalability of ABM simulations is typically limited due to the computationally expensive nature of simulating a large number of individuals. As such, large scale ABM simulations are excellent candidates to apply parallel computing approaches such as Graphics Processing Units (GPUs). In this paper, we present an extension to the FLAME GPU 1 [1] framework which addresses the divergence problem, i.e. the challenge of executing the behaviour of non-homogeneous individuals on vectorised GPU processors. We do this by describing a modelling methodology which exposes inherent parallelism within the model which is exploited by novel additions to the software permitting higher levels of concurrent simulation execution. Moreover, we demonstrate how this extension can be applied to realistic cellular level tissue model by benchmarking the model to demonstrate a measured speedup of over 4x

Testing Based on Identifiable P Systems Using Cover Automata and X-Machines

YesThis paper represents a significant advance on the issue of testing for implementations specified by P systems with transformation and communicating rules. Using the X-machine framework and the concept of cover automaton, it devises a testing approach for such systems, that, under well defined conditions, it ensures that the implementation conforms to the specification. It also investigates the issue of identifiability for P systems, that is an essential prerequisite for testing implementations based on such specifications and establishes a fundamental set of properties for identifiable P systems.Marian Gheorghe and Savas Konur acknowledge the support from EPSRC (EP/I031812/1). Marian Gheorghe’s and Florentin Ipate’s work is partially supported by CNCS-UEFISCDI (PN-II-ID-PCE-2011-3-0688)

Binding and Antigen Presentation of Ceramide-Containing Glycolipids by Soluble Mouse and Human Cd1d Molecules

We have purified soluble mouse and human CD1d molecules to assess the structural requirements for lipid antigen presentation by CD1. Plate-bound CD1d molecules from either species can present the glycolipid α-galactosyl ceramide (α-GalCer) to mouse natural killer T cells, formally demonstrating both the in vitro formation of antigenic complexes, and the presentation of α-GalCer by these two CD1d molecules. Using surface plasmon resonance, we show that at neutral pH, mouse CD1 and human CD1d bind to immobilized α-GalCer, unlike human CD1b, which requires acidic pH for lipid antigen binding. The CD1d molecules can also bind both to the nonantigenic β-GalCer and to phosphatidylethanolamine, indicating that diverse lipids can bind to CD1d. These studies provide the first quantitative analysis of monomeric lipid antigen–CD1 interactions, and they demonstrate that the orientation of the galactose, or even the nature of the polar head group, are likely to be more important for T cell receptor contact than CD1d binding

Torsional angle dependence and switching of inner sphere reorganisation energies for electron and hole charge transfer processes involving phenyl substituted diketopyrrolopyrroles; a density functional study

This document is the Accepted Manuscript version of the following article: Jesus Calvo-Castro, Callum J. McHugh, Andrew J. McLean, ‘Torsional angle dependence and switching of inner sphere reorganisation energies for electron and hole transfer processes involving phenyl substituted diketopyrrolopyrroles; a density functional study’, Dyes and Pigments, Vol. 113, pp. 609-617, February 2015. The Version of Record is available online at doi: https://doi.org/10.1016/j.dyepig.2014.09.031. Published by Elsevier.Determination of inner sphere reorganisation energies is important in the development of organic charge mediating materials and electron transfer reactions. In this study, hole and electron inner sphere reorganisation energies, lambda(h) and lambda(e) respectively, have been computed for the first time for a series of structurally related diketopyrrolopyrrole (DPP) molecular motifs. Inner sphere reorganisation energies for self-exchange electron transfer reactions are calculated as being lower than those associated hole transfer processes in model planar phenyl and thiophenyl substituted DPP systems. It is found that lambda(e) lambda(h).Peer reviewedFinal Accepted Versio

Tamoxifen for prevention of breast cancer: extended long-term follow-up of the IBIS-I breast cancer prevention trial

© Cuzick et al. Open Access article distributed under the terms of CC BY.http://dx.doi.org/10.1016/S1470-2045(14)71171-

Vascular density and phenotype around ductal carcinoma in situ (DCIS) of the breast

Up to 50% of recurrences of ductal carcinoma in situ of the breast are associated with invasive carcinoma but no pathological or molecular features have yet been found to predict for the development of invasive disease. For a tumour to invade, it requires the formation of new blood vessels. Previous studies have described a vascular rim around ducts involved by ductal carcinoma in situ, raising the possibility that the characteristics of periductal vascularisation may be important in determining transformation from in situ to invasive disease. Periductal vascular density and phenotype were determined using morphometry and a panel of anti-endothelial antibodies (von Willebrand factor, CD31, CD141 and CD34) and related to the presence of invasive carcinoma and other histological features. Compared to normal lobules, pure ductal carcinoma in situ exhibited a greater density of CD34+ and CD31+ vessels but a decrease in those that were immunopositive for vWF, indicating a difference in phenotype and in density. Ductal carcinoma in situ associated with invasive carcinoma showed a profile of vascular immunostaining similar to that of pure ductal carcinoma in situ but there were significantly greater numbers of CD34+ and CD141+ vessels and fewer staining for vWF. There was a significant negative correlation between vascular density and both the cross-sectional areas of the ducts involved and the extent of the necrosis of the tumour they contained. A correlation between vascular density and nuclear grade was also noted, being highest in the intermediate grade. The greater density of CD34+ and CD141+ vessels around ductal carcinoma in situ associated with invasive carcinoma could reflect a greater predisposition to invade but a direct effect of co-existent invasive carcinoma cannot entirely be ruled out in the present study. The relationship between vascular density, grade, duct size and nuclear grade suggests that periductal angiogenesis increases with tumour growth rate but is unable to keep pace with the most rapidly growing lesions