Extensible Technology-Agnostic Runtime Verification

With numerous specialised technologies available to industry, it has become increasingly frequent for computer systems to be composed of heterogeneous components built over, and using, different technologies and languages. While this enables developers to use the appropriate technologies for specific contexts, it becomes more challenging to ensure the correctness of the overall system. In this paper we propose a framework to enable extensible technology agnostic runtime verification and we present an extension of polyLarva, a runtime-verification tool able to handle the monitoring of heterogeneous-component systems. The approach is then applied to a case study of a component-based artefact using different technologies, namely C and Java.Comment: In Proceedings FESCA 2013, arXiv:1302.478

Structural and electronic models of the water oxidizing complex in the S 0 state of photosystem II: a density functional study

Large size (228 atom, 229 atom for protonated form) molecular models of the oxygen evolving complex of photosystem II (OEC), with a complete set of ligating aminoacids, the redox-active tyrosine YZ, and proton/water transfer channels terminating at the water oxidizing Mn/Ca cluster, are constructed based on the highest available resolution X-ray diffraction structures of the protein and our previous density functional theory (DFT) studies of isolated metal cluster model structures. Geometries optimized using the general gradient approximation (GGA) or hybrid density functionals are compared with high-resolution extended X-ray absorption fine structure (EXAFS) spectroscopic data and show that an antiferromagnetic configuration of the Mn centers in the cluster gives computed metal-metal distances in excellent agreement with experiment. The excitation energies predicted by time-dependent density functional theory (TDDFT) calculations for truncated 106 atom and 78 atom structures derived from the large models show that a previously proposed III-III-III-II oxidation pattern of the Mn atoms agrees very well with the X-ray absorption near-edge structure (XANES) observed for the S0 state of the OEC. This supports a "low" Mn oxidation state paradigm for the OEC, when a realistic protein imposed environment for the catalytic metal cluster is used in calculations. The probable protonation sites in the cluster and roles of the proton/water transfer channels are discussed in light of the computational results

Runtime monitoring of distributed systems

Distributed and component-based architectures are becoming more prevalent computer systems. The increased complexities introduced by the distribution hampers dependability, emphasising the need for verification techniques tailored for a distributed setting. Runtime verification has proven to be a viable approach for verifying correctness, by focussing on the adherence of the runtime-generated trace to the desired properties. We present a broad taxonomy of current techniques to distributed monitoring, culminating in the proposal of a novel migrating monitor approach. We argue for certain situations where this approach presents clear advantages over current techniques.peer-reviewe

Distributed system contract monitoring

Runtime verification of distributed systems poses various challenges. A pivotal challenge is the choice of how to distribute the monitors themselves across the system. On one hand, centralised monitoring may result in increased communication overhead and information exposure across locations, while, on the other hand, systems with dynamic topologies and properties are difficult to address using static monitor choreographies. In this paper we present mDPi, a location-aware π-calculus extension for reasoning about the distributed monitoring scenario. We also define numerous monitoring strategies for a regular expression-based logic, including a novel approach in which monitors migrate to ensure local monitoring. Finally, we present a number of results which emerge from this formalism, justifying our approach.peer-reviewe

Considerations for monitoring highly concurrent systems

Sequential monitoring tools such as Larva are impractical for monitoring highly concurrent systems such as online establishments handling hundreds of transactions a second — they lock valuable resources which may otherwise be used to serve valid user requests. In the context of an open-source e-commerce system, we discuss design issues involved in allowing monitors to run concurrently while at the same time ensuring that they remain correct: free from race conditions and faithful to the properties they embody.peer-reviewe

Gullain-Barre’ syndrome post-SARS-CoV-2 in Malta : a case report

A 70-year-old lady presented three weeks after a mild SARS-CoV-2 infection with a nine-day history of worsening back pain, progressive lower limb weakness and paraesthesia, dysphagia, constipation and difficulty in completing full sentences. Outcome of her investigations were in keeping with a diagnosis of acute inflammatory demyelinating polyneuropathy. The patient made a rapid and full recovery after treatment with intravenous immunoglobulins (IVIG).peer-reviewe

Simplifying Contract-Violating Traces

Contract conformance is hard to determine statically, prior to the deployment of large pieces of software. A scalable alternative is to monitor for contract violations post-deployment: once a violation is detected, the trace characterising the offending execution is analysed to pinpoint the source of the offence. A major drawback with this technique is that, often, contract violations take time to surface, resulting in long traces that are hard to analyse. This paper proposes a methodology together with an accompanying tool for simplifying traces and assisting contract-violation debugging.Comment: In Proceedings FLACOS 2012, arXiv:1209.169

Compensations in an imperative programming language

Numerous mechanisms are used to deal with failure of sys- tems or processes, one of which is that of compensating ac- tions. A compensation can be seen as a program which somehow cancels out the effects of another — and by or- ganising code in such a way so as to associate each program with its compensation, enables implicit recovery to a sane state if part of a computation somehow fails. In this paper we present an imperative programming language natively supporting the notion of compensations, thus enabling the programmer to program using a notion of compensations at the source level of the system under development.peer-reviewe

Interactive Whole-Heart Segmentation in Congenital Heart Disease

We present an interactive algorithm to segment the heart chambers and epicardial surfaces, including the great vessel walls, in pediatric cardiac MRI of congenital heart disease. Accurate whole-heart segmentation is necessary to create patient-specific 3D heart models for surgical planning in the presence of complex heart defects. Anatomical variability due to congenital defects precludes fully automatic atlas-based segmentation. Our interactive segmentation method exploits expert segmentations of a small set of short-axis slice regions to automatically delineate the remaining volume using patch-based segmentation. We also investigate the potential of active learning to automatically solicit user input in areas where segmentation error is likely to be high. Validation is performed on four subjects with double outlet right ventricle, a severe congenital heart defect. We show that strategies asking the user to manually segment regions of interest within short-axis slices yield higher accuracy with less user input than those querying entire short-axis sliceNatural Sciences and Engineering Research Council of Canada (Alexander Graham Bell Canada Graduate Scholarships-Doctoral Program (CGS D))Wistron CorporationNational Institute for Biomedical Imaging and Bioengineering (U.S.) (NAMIC U54-EB005149)Boston Children's Hospital (Translational Research Program Fellowship)Boston Children's Hospital. Office of Faculty DevelopmentHarvard Catalys