A monotone framework for CCS

The calculus of communicating systems, CCS, was introduced by Robin Milner as a calculus for modelling concurrent systems. Subsequently several techniques have been developed for analysing such models in order to get further insight into their dynamic behaviour.In this paper we present a static analysis for approximating the control structure embedded within the models. We formulate the analysis as an instance of a monotone framework and thus draw on techniques that often are associated with the efficient implementation of classical imperative programming languages.We show how to construct a finite automaton that faithfully captures the control structure of a CCS model. Each state in the automaton records a multiset of the enabled actions and appropriate transfer functions are developed for transforming one state into another. A classical worklist algorithm governs the overall construction of the automaton and its termination is ensured using techniques from abstract interpretation.     

Mikrobielle Werkstoffzerstörung – Biofilm und Biofouling: Bekämpfung von Biofouling in wäßrigen Systemen

Microbial deterioration of materials – biofilm und biofouling: Countermeasures against biofouling in water systems Countermeasures against biofouling include three steps: i) detection, ii) sanitization and iii) prevention of biofouling. The detection has to refer to surfaces. Cell counts in water samples do not reflect site or extent of biofilms. Biocides display only limited value in terms of removal of biofouling layers. First, biofilm organisms are protected against biocides and tolerate 10–1000 fold higher concentrations. Second, water systems usually cannot be kept sterile. Thus, dead biofilms provide nutrients and suitable surfaces for further growth of cells imported with the raw water. Cleaning of a system is an integral part of sanitization and even more important than disinfection. It has to base on a designed strategy. Efficiency control is mandatory, which has to occur on representative surfaces. The prevention of biofouling is frequently achieved by continuously dosage of biocides. This is, however, only possible with suitable raw waters and many failures are reported. Chlorine is still the biocide most frequently used. Reasons of effectivity and environmental protection give rise to other strategies. “Good housekeeping” is recommended as countermeasure. It consists of frequent cleaning, efficiency control, biofilm monitoring, limitation of nutrients, maintenance of high shear forces and a cleaning-friendly design.     

Control Flow Analysis for BioAmbients

This paper presents a static analysis for investigating properties of biological systems specified in BioAmbients. We exploit the control flow analysis to decode the bindings of variables induced by communications and to build a relation of the ambients that can interact with each other. We eventually apply our analysis to an example of gene regulation by positive feedback taken from the literature.     

Using 15N‐Ammonium to Characterise and Map Potassium Binding Sites in Proteins by NMR Spectroscopy

A variety of enzymes are activated by the binding of potassium ions. The potassium binding sites of these enzymes are very specific, but ammonium ions can often replace potassium ions in vitro because of their similar ionic radii. In these cases, ammonium can be used as a proxy for potassium to characterise potassium binding sites in enzymes: the ¹H,¹⁵N spin‐pair of enzyme‐bound ¹⁵NH₄⁺ can be probed by ¹⁵N‐edited heteronuclear NMR experiments. Here, we demonstrate the use of NMR spectroscopy to characterise binding of ammonium ions to two different enzymes: human histone deacetylase 8 (HDAC8), which is activated allosterically by potassium, and the bacterial Hsp70 homologue DnaK, for which potassium is an integral part of the active site. Ammonium activates both enzymes in a similar way to potassium, thus supporting this non‐invasive approach. Furthermore, we present an approach to map the observed binding site onto the structure of HDAC8. Our method for mapping the binding site is general and does not require chemical shift assignment of the enzyme resonances.     

Noninvasive estimation of dynamic pressures in vitro and in vivo using the subharmonic response from microbubbles

The purpose of this study was to develop and validate a noninvasive pressure estimation technique based on subharmonic emissions from a commercially available ultrasound contrast agent and scanner, unlike other studies that have either adopted a single-element transducer approach and/ or use of in-house contrast agents. Ambient pressures were varied in a closed-loop flow system between 0 and 120 mmHg and were recorded by a solid-state pressure catheter as the reference standard. Simultaneously, the ultrasound scanner was operated in pulse inversion mode transmitting at 2.5 MHz, and the unprocessed RF data were captured at different incident acoustic pressures (from 76 to 897 kPa). The subharmonic data for each pulse were extracted using band-pass filtering with averaging, and subsequently processed to eliminate noise. The incident acoustic pressure most sensitive to ambient pressure fluctuations was determined, and then the ambient pressure was tracked over 20 s. In vivo validation of this technique was performed in the left ventricle (LV) of 2 canines. In vitro, the subharmonic signal could track ambient pressure values with r(2) = 0.922 (p < 0.001), whereas in vivo, the subharmonic signal tracked the LV pressures with r(2) > 0.790 (p < 0.001) showing a maximum error of 2.84 mmHg compared with the reference standard. In conclusion, a subharmonic ultrasound-based pressure estimation technique, which can accurately track left ventricular pressures, has been established.     

Comparison of three methods for detection of herbal food supplement irradiation

A survey for irradiation of 106 herbal food supplements was carried out in Denmark in 2003. The results from three methods, two screening methods and a specific method, were compared: Direct epifluorescent filter technique/aerobic plate count (DEFT/APC), photostimulated luminescence (PSL) and thermoluminescence (TL) standardised by Comité Européen de Normalisation (CEN). Forty samples screened positive with the DEFT/APC method. However, the TL method could only confirm irradiation of 15 samples, 11 samples wholly irradiated and 4 samples with a minor irradiated ingredient. Thus, the DEFT/APC method gave a large number of false positive results, although the number of false negative results probably was very low. Only 7 of the 15 confirmed irradiated samples screened positive with the PSL screening method, the samples with low photon counts escaping detection. For 10% of the samples also the TL method was lacking in sensitivity, as not enough minerals could be isolated to get a signal over the minimum detection level. For such clean herbal food supplements no suitable method exists at all among the CEN standardised methods for irradiation detection.     

Active Evaluation Contexts for Reaction Semantics

In the context of process algebras it is customary to define semantics in the form of a reaction relation supported by a structural congruence relation. Recently process algebras have grown more expressive in order to meet the modelling demands of fields as diverse as business modelling and systems biology. This leads to combining various features, such as general choice and parallelism that were previously studied separately, and it often becomes difficult to define the reaction semantics. We present a general approach based on active evaluation contexts that allows the reaction semantics to be easily constructed.