Phylogenetic scanning: a computer-assisted algorithm for mapping gene conversions and other recombinational events

An algorithm, 'phylogenetic scanning', is described for mapping gene conversion events where comparative DNA sequence data are available from different species. In this algorithm, sets of hypothetical phylogenetic trees are constructed that describe possible sequence relationships due to gene conversions in different species lineages; these trees are then evaluated by the principle of parsimony at intervals in the sequence alignment. When used to map gene conversion events that occurred between the pair of gamma-globin genes of higher primates, the algorithm gives results nearly identical to those obtained using a tedious manual approach. Suggestions are also provided for adaptation of this procedure to the analysis of other recombination events.     

Resource contention in shared-memory multiprocessors: A parameterized performance degradation model

A standard metric conventionally employed to compare the performance of different multiprocessor systems is speedup. Although providing a measure of the improvement in execution speed achievable on a system, this metric does not yield any insight into the factors responsible for limiting the potential improvement in speed. This paper studies the performance degradation in shared-memory multiprocessors as a result of contention for shared-memory resources. A replicate workload framework with a flexible mechanism for workload specification is proposed for measuring performance. Two normalized performance metrics—efficiency and overhead factor—are introduced to quantify the factors limiting performance and facilitate comparison across architectures. Finally, the proposed model is employed to measure and compare the performance of three contemporary shared-memory systems, with special emphasis on the newly released BBN Butterfly-II (TC2000), currently undergoing Beta test.     

A proof system for communicating processes with value-passing

A proof system for a version of CCS with value-passing is proposed in which the reasoning about data is factored out from that about the structure of processes. The system is shown to be sound and complete for finite terms with respect to a denotational semantics based on Acceptance Trees.     

Uniform and optimal schemes for stiff initial-value problems

We formulate a class of difference schemes for stiff initial-value problems, with a small parameter ε multiplying the first derivative. We derive necessary conditions for uniform convergence with respect to the small parameter ε, that is the solution of the difference scheme u_i^h satisfies |u_i^h−u(x_i)| Ch, where C is independent of h and ε. We also derive sufficient conditions for uniform convergence and show that a subclass of schemes is also optimal in the sense that |u_i^h−u(x_i)| C min (h, ε). Finally, we show that this class contains higher-order schemes.     

Quality-Assurance Technology in Japan

A survey of the state of SQA in Japan finds that the situation is much like, but slightly different than, that in the US.