A Branching Time Model of CSP

I present a branching time model of CSP that is finer than all other models of CSP proposed thus far. It is obtained by taking a semantic equivalence from the linear time - branching time spectrum, namely divergence-preserving coupled similarity, and showing that it is a congruence for the operators of CSP. This equivalence belongs to the bisimulation family of semantic equivalences, in the sense that on transition systems without internal actions it coincides with strong bisimilarity. Nevertheless, enough of the equational laws of CSP remain to obtain a complete axiomatisation for closed, recursion-free terms.Comment: Dedicated to Bill Roscoe, on the occasion of his 60th birthda

Microwave Radar-Based Breast Cancer Detection:Imaging in Inhomogeneous Breast Phantoms

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On pairwise distances and median score of three genomes under DCJ

In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a resulting genome is called median genome). In contrast to the rearrangement distance between two genomes which can be computed in linear time, computing the median score for three genomes is NP-hard. This inspires a quest for simpler and faster approximations for the median score, the most natural of which appears to be the halved sum of pairwise distances which in fact represents a lower bound for the median score. In this work, we study relationship and interplay of pairwise distances between three genomes and their median score under the model of Double-Cut-and-Join (DCJ) rearrangements. Most remarkably we show that while a rearrangement may change the sum of pairwise distances by at most 2 (and thus change the lower bound by at most 1), even the most "powerful" rearrangements in this respect that increase the lower bound by 1 (by moving one genome farther away from each of the other two genomes), which we call strong, do not necessarily affect the median score. This observation implies that the two measures are not as well-correlated as one's intuition may suggest. We further prove that the median score attains the lower bound exactly on the triples of genomes that can be obtained from a single genome with strong rearrangements. While the sum of pairwise distances with the factor 2/3 represents an upper bound for the median score, its tightness remains unclear. Nonetheless, we show that the difference of the median score and its lower bound is not bounded by a constant.Comment: Proceedings of the 10-th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG), 2012. (to appear

Stress dependent thermal pressurization of a fluid-saturated rock

Temperature increase in saturated porous materials under undrained conditions leads to thermal pressurization of the pore fluid due to the discrepancy between the thermal expansion coefficients of the pore fluid and of the solid matrix. This increase in the pore fluid pressure induces a reduction of the effective mean stress and can lead to shear failure or hydraulic fracturing. The equations governing the phenomenon of thermal pressurization are presented and this phenomenon is studied experimentally for a saturated granular rock in an undrained heating test under constant isotropic stress. Careful analysis of the effect of mechanical and thermal deformation of the drainage and pressure measurement system is performed and a correction of the measured pore pressure is introduced. The test results are modelled using a non-linear thermo-poro-elastic constitutive model of the granular rock with emphasis on the stress-dependent character of the rock compressibility. The effects of stress and temperature on thermal pressurization observed in the tests are correctly reproduced by the model

Liquid PTVA: A faster and cheaper alternative for generating multi-copy clones in Pichia pastoris

Additional file 1: Figure S1. Schematic representation of the expression vectors pZGFP, pZÎąGFP, pKGFP and pKÎąGFP

HIV infection and domestic smoke exposure, but not human papillomavirus, are risk factors for esophageal squamous cell carcinoma in Zambia: a case-control study

(c) 2015 The Authors. Cancer Medicine published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

An implementation of Deflate in Coq

The widely-used compression format "Deflate" is defined in RFC 1951 and is based on prefix-free codings and backreferences. There are unclear points about the way these codings are specified, and several sources for confusion in the standard. We tried to fix this problem by giving a rigorous mathematical specification, which we formalized in Coq. We produced a verified implementation in Coq which achieves competitive performance on inputs of several megabytes. In this paper we present the several parts of our implementation: a fully verified implementation of canonical prefix-free codings, which can be used in other compression formats as well, and an elegant formalism for specifying sophisticated formats, which we used to implement both a compression and decompression algorithm in Coq which we formally prove inverse to each other -- the first time this has been achieved to our knowledge. The compatibility to other Deflate implementations can be shown empirically. We furthermore discuss some of the difficulties, specifically regarding memory and runtime requirements, and our approaches to overcome them

Beyond Node Degree: Evaluating AS Topology Models

This is the accepted version of 'Beyond Node Degree: Evaluating AS Topology Models', archived originally at arXiv:0807.2023v1 [cs.NI] 13 July 2008.Many models have been proposed to generate Internet Autonomous System (AS) topologies, most of which make structural assumptions about the AS graph. In this paper we compare AS topology generation models with several observed AS topologies. In contrast to most previous works, we avoid making assumptions about which topological properties are important to characterize the AS topology. Our analysis shows that, although matching degree-based properties, the existing AS topology generation models fail to capture the complexity of the local interconnection structure between ASs. Furthermore, we use BGP data from multiple vantage points to show that additional measurement locations significantly affect local structure properties, such as clustering and node centrality. Degree-based properties, however, are not notably affected by additional measurements locations. These observations are particularly valid in the core. The shortcomings of AS topology generation models stems from an underestimation of the complexity of the connectivity in the core caused by inappropriate use of BGP data