Weak refinement in Z

An important aspect in the specification of distributed systems is the role of the internal (or unobservable) operation. Such operations are not part of the user interface (i.e. the user cannot invoke them), however, they are essential to our understanding and correct modelling of the system. Various conventions have been employed to model internal operations when specifying distributed systems in Z. If internal operations are distinguished in the specification notation, then refinement needs to deal with internal operations in appropriate ways. However, in the presence of internal operations, standard Z refinement leads to undesirable implementations. In this paper we present a generalization of Z refinement, called weak refinement, which treats internal operations differently from observable operations when refining a system. We illustrate some of the properties of weak refinement through a specification of a telecommunications protocol

Formal Specification and Testing of a Management Architecture

The importance of network and distributed systems management to supply and maintain services required by users has led to a demand for management facilities. Open network management is assisted by representing the system resources to be managed as objects, and providing standard services and protocols for interrogating and manipulating these objects. This paper examines the application of formal description techniques to the specification of managed objects by presenting a case study in the specification and testing of a management architecture. We describe a formal specification of a management architecture suitable for scheduling and distributing services across nodes in a distributed system. In addition, we show how formal specifications can be used to generate conformance tests for the management architecture

LP 133-373: A New Chromospherically Active Eclipsing dMe Binary with a Distant, Cool White Dwarf Companion

We report the discovery of the partially eclipsing binary LP 133-373. Nearly identical eclipses along with observed photometric colors and spectroscopy indicate that it is a pair of chromospherically active dM4 stars in a circular 1.6 day orbit. Light and velocity curve modeling to our differential photometry and velocity data show that each star has a mass and radius of 0:340 ± 0:014 MꙨ and 0:33 ± 0:02 RꙨ. The binary is itself part of a common proper motion pair with LP 133-374, a cool DC or possible DA white dwarf with a mass of 0.49Y0.82 MꙨ, which would make the system at least 3 Gyr old

Spectroscopic and photometric analysis of HS 1136+6646: A hot young DAO+K7V post-common- envelope, pre-cataclysmic variable binary

Copyright © 2004 IOP Publishing / American Astronomical SocietyExtensive photometric and spectroscopic observations have been obtained for HS 1136+6646. The observations reveal a newly formed post–common-envelope binary system containing a hot ~DAO.5 primary and a highly irradiated secondary. HS 1136+6646 is the most extreme example yet of a class of short-period hot H-rich white dwarfs with K–M companion systems such as V471 Tau and Feige 24. HS 1136+6646 is a double-line spectroscopic binary showing emission lines of H I, He II, C II, Ca II, and Mg II, due in part to irradiation of the K7 V secondary by the hot white dwarf. Echelle spectra reveal the hydrogen emission lines to be double-peaked with widths of ~200 km s-1, raising the possibility that emission from an optically thin disk may also contribute. The emission lines are observed to disappear near the inferior conjunction. An orbital period of 0.83607 ± 0.00003 days has been determined through the phasing of radial velocities, emission-line equivalent widths, and photometric measurements spanning a range of 24 months. Radial velocity measurements yield an amplitude of KWD = 69 ± 2 km s-1 for the white dwarf and KK7V = 115 ± 1 km s-1 for the secondary star. In addition to orbital variations, photometric measurements have also revealed a low-amplitude modulation with a period of 113.13 minutes and a semiamplitude of 0.0093 mag. These short-period modulations are possibly associated with the rotation of the white dwarf. From fits of the Balmer line profiles, the white dwarf is estimated to have an effective temperature and gravity of ~70,000 K and log g ~ 7.75, respectively. However, this optically derived temperature is difficult to reconcile with the far-UV spectrum of the Lyman line region. Far Ultraviolet Spectroscopic Explorer spectra show the presence of O VI absorption lines and a spectral energy distribution whose slope persists nearly to the Lyman limit. The extremely high temperature of the white dwarf, from both optical and UV measurements, indicates that the binary system is one of the earliest post–common-envelope objects known, having an age around 7.7 × 105 yr. Although the spectrum of the secondary star is best represented by a K7 V star, indications are that the star may be overly luminous for its mass.NASAParticle and Astronomy Research Council, UKNS

EXACT2: the semantics of biomedical protocols

© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources

Redeploying β-lactam antibiotics as a novel antivirulence strategy for the treatment of methicillin-resistant <i>Staphylococcus aureus</i> infections

Innovative approaches to the use of existing antibiotics is an important strategy in efforts to address the escalating antimicrobial resistance crisis. We report a new approach to the treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections by demonstrating that oxacillin can be used to significantly attenuate the virulence of MRSA despite the pathogen being resistant to this drug. Using mechanistic in vitro assays and in vivo models of invasive pneumonia and sepsis, we show that oxacillin-treated MRSA strains are significantly attenuated in virulence. This effect is based primarily on the oxacillin-dependent repression of the accessory gene regulator quorum-sensing system and altered cell wall architecture, which in turn lead to increased susceptibility to host killing of MRSA. Our data indicate that beta-lactam antibiotics should be included in the treatment regimen as an adjunct antivirulence therapy for patients with MRSA infections. This would represent an important change to current clinical practice for treatment of MRSA infection, with the potential to significantly improve patient outcomes in a safe, cost-effective manner

Novel insights into host-fungal pathogen interactions derived from live-cell imaging

Acknowledgments The authors acknowledge funding from the Wellcome Trust (080088, 086827, 075470 and 099215) including a Wellcome Trust Strategic Award for Medical Mycology and Fungal Immunology 097377 and FP7-2007–2013 grant agreement HEALTH-F2-2010-260338–ALLFUN to NARG.Peer reviewedPublisher PD