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

Quantum atomic delocalization vs. structural disorder in amorphous silicon

Quantum effects on the atom delocalization in amorphous silicon have been studied by path-integral Monte Carlo simulations from 30 to 800 K. The quantum delocalization is appreciable vs. topological disorder, as seen from structural observables such as the radial distribution function (RDF). At low temperatures, the width of the first peak in the RDF increases by a factor of 1.5 due to quantum effects. The overall anharmonicity of the solid vibrations at finite temperatures in amorphous silicon is clearly larger than in the crystalline material. Low-energy vibrational modes are mainly located on coordination defects in the amorphous material.Comment: 5 pages, 5 PS figures, REVTE

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

Quantum wires from coupled InAs/GaAs strained quantum dots

The electronic structure of an infinite 1D array of vertically coupled InAs/GaAs strained quantum dots is calculated using an eight-band strain-dependent k-dot-p Hamiltonian. The coupled dots form a unique quantum wire structure in which the miniband widths and effective masses are controlled by the distance between the islands, d. The miniband structure is calculated as a function of d, and it is shown that for d>4 nm the miniband is narrower than the optical phonon energy, while the gap between the first and second minibands is greater than the optical phonon energy. This leads to decreased optical phonon scattering, providing improved quantum wire behavior at high temperatures. These miniband properties are also ideal for Bloch oscillation.Comment: 5 pages revtex, epsf, 8 postscript figure

Distinct Contribution of DNA Methylation and Histone Acetylation to the Genomic Occupancy of Transcription Factors

Abstract Epigenetic modifications on chromatin play important roles in regulating gene expression. While chromatin states are often governed by multi-layered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase complexes (HDACs). Both of these mechanisms can potentially affect gene expression, but the importance of each, and whether these activities are integrated to achieve appropriate gene regulation, remains largely unknown. To address this important question, we measured gene expression, chromatin accessibility, and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. Interestingly, we observe widespread increases in chromatin accessibility at repeat elements when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset of these elements have elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced additive effect of HDAC inhibition in DNA methylation deficient cells demonstrate that DNA methylation and histone deacetylation act largely independently to suppress transcription factor binding and gene expression

Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors

Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase complexes (HDACs). Both of these mechanisms can potentially affect gene expression, but the importance of each, and whether these activities are integrated to achieve appropriate gene regulation, remains largely unknown. To address this important question, we measured gene expression, chromatin accessibility, and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. We observe widespread increases in chromatin accessibility at retrotransposons when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset of these elements has elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced additive effect of HDAC inhibition in DNA methylation-deficient cells demonstrates that DNA methylation and histone deacetylation act largely independently to suppress transcription factor binding and gene expression

Structure, Stresses and Local Dynamics in Glasses

The interrelations between short range structural and elastic aspects in glasses and glass forming liquids pose important and yet unresolved questions. In this paper these relations are analyzed for mono-atomic glasses and stressed liquids with a short range repulsive-attractive pair potentials. Strong variations of the local pressure are found even in a zero temperature glass, whereas the largest values of pressure are the same in both glasses and liquids. The coordination number z(J) and the effective first peak radius depend on the local pressures J's. A linear relation was found between components of site stress tensor and the local elastic constants. A linear relation was also found between the trace of the squares of the local frequencies and the local pressures. Those relations hold for glasses at zero temperature and for liquids. We explain this by a relation between the structure and the potential terms. A structural similarity between liquids and solids is manifested by similar dependencies of the coordination number on the pressures.Comment: 7 pages, 11 figure

Successful recruitment to trials: findings from the SCIMITAR plus Trial

BACKGROUND: Randomised controlled trials (RCT) can struggle to recruit to target on time. This is especially the case with hard to reach populations such as those with severe mental ill health. The SCIMITAR+ trial, a trial of a bespoke smoking cessation intervention for people with severe mental ill health achieved their recruitment ahead of time and target. This article reports strategies that helped us to achieve this with the aim of aiding others recruiting from similar populations. METHODS: SCIMITAR+ is a multi-centre pragmatic two-arm parallel-group RCT, which aimed to recruit 400 participants with severe mental ill health who smoke and would like to cut down or quit. The study recruited primarily in secondary care through community mental health teams and psychiatrists with a smaller number of participants recruited through primary care. Recruitment opened in October 2015 and closed in December 2016, by which point 526 participants had been recruited. We gathered information from recruiting sites on strategies which led to the successful recruitment in SCIMITAR+ and in this article present our approach to trial management along with the strategies employed by the recruiting sites. RESULTS: Alongside having a dedicated trial manager and trial management team, we identified three main themes that led to successful recruitment. These were: clinicians with a positive attitude to research; researchers and clinicians working together; and the use of NHS targets. The overriding theme was the importance of relationships between both the researchers and the recruiting clinicians and the recruiting clinicians and the participants. CONCLUSIONS: This study makes a significant contribution to the limited evidence base of real-world cases of successful recruitment to RCTs and offers practical guidance to those planning and conducting trials. Building positive relationships between clinicians, researchers and participants is crucial to successful recruitment

Propylene Carbonate Reexamined: Mode-Coupling β\beta Scaling without Factorisation ?

The dynamic susceptibility of propylene carbonate in the moderately viscous regime above $T_{\rm c}$ is reinvestigated by incoherent neutron and depolarised light scattering, and compared to dielectric loss and solvation response. Depending on the strength of $\alpha$ relaxation, a more or less extended $\beta$ scaling regime is found. Mode-coupling fits yield consistently $\lambda=0.72$ and $T_{\rm c}=182$K, although different positions of the susceptibility minimum indicate that not all observables have reached the universal asymptotics