Duncan J Clarke

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Metaphase chromatids are believed to consist of loops of chromatin anchored to a central scaffold, of which a major component is the decatenatory enzyme DNA topoisomerase II. Silver impregnation selectively stains an axial element of metaphase and anaphase chromatids; but we find that in earlier stages of mitosis, silver staining reveals an initially(More)
The enzyme DNA topoisomerase II, which removes the catenations formed between the DNA molecules of sister chromatids during replication and is a structural component of chromosome cores, is needed for chromosome condensation in yeast and in Xenopus extracts. Inhibitors of topoisomerase II arrest mammalian cells before mitosis in the G2 phase of the cell(More)
Rad23 is a highly conserved protein involved in nucleotide excision repair (NER) that associates with the proteasome via its N-terminus. Its C-terminal ubiquitin-associated (UBA) domain is evolutionarily conserved from yeast to humans. However, the cellular function of UBA domains is not completely understood. Recently, RAD23 and DDI1, both DNA(More)
We report on a tool we have developed that implements conformance testing techniques to automatically derive symbolic tests cases from formal operational specifications. We demonstrate the application of the techniques and tools on a simple example and present case studies for the CEPS (Common Electronic Purse Specification) and for the file system of the(More)
The Saccharomyces cerevisiae genes RAD23 and DDI1 were identified in a screen for multicopy suppressors of the temperature-sensitivity of a mutant allele of S. cerevisiae PDS1. Pds1 is a regulator of anaphase that needs to accumulate and then be degraded by the ubiquitin-proteasome pathway at the metaphase-anaphase transition for cells to progress normally(More)
The S-phase checkpoint kinases Mec1 and Rad53 in the budding yeast, Saccharomyces cerevisiae, are activated in response to replication stress that induces replication fork arrest. In the absence of a functional S-phase checkpoint, stalled replication forks collapse and give rise to chromosome breakage. In an attempt to better understand replication dynamics(More)
Although the use of performance efficiency measures (speed, movement economy, errors) and ergonomic assessments are relatively well established, the evaluation of cognitive outcomes is rare. This report makes the case for assessment strategies that include mental workload measures as a way to improve training scenarios and training/operating environments.(More)
In Saccharomyces cerevisiae, the metaphase-anaphase transition is initiated by the anaphase-promoting complex-dependent degradation of Pds1, whereby Esp1 is activated to promote sister chromatid separation. Although this is a fundamental step in the cell cycle, little is known about the regulation of Esp1 and how loss of cohesion is coordinated with(More)
The paper discusses the use of formal methods for the analysis of architectural models expressed in the modeling language AADL. AADL describes the system as a collection of interacting components. The AADL standard prescribes semantics for the thread components and rules of interaction between threads and other components in the system. We present a(More)
To engineer reliable real-time systems, it is desirable to detect timing anomalies early in the development process. However, there is little work addressing the problem of accurately predicting timing properties of real-time systems before implementations are developed. This paper describes an approach to the specification and schedulability analysis of(More)