Apex graph grammars and attribute grammars

Summary Apex graph grammars are a particular type of directed node-label controlled (DNLC) graph grammars: the embedding edges are established between terminal nodes only. Apex graph grammars, slightly generalized, can generate the sets of dependency graphs of attribute grammars. The other way around, every apex graph language can be obtained from such a dependency graph language by a graph replacement (which is an operation analogous to a string homomorphism).     

Iterated deterministic substitution

Summary Deterministic substitution of languages means substituting the same word (from a given language) for all occurrences of a symbol. For an arbitrary family K of languages the notion of deterministic K-iteration grammar is introduced, which is essentially the iteration of a finite number of deterministic substitutions of languages from K. The families of languages generated by these grammars are investigated.The work of the first author has been supported by the Netherlands Organization for the Advancement of Pure Research (Z.W.O.)     

Nephrotoxicity of cephaloridine in newborn rabbits: role of the renal anionic transport system

The nephrotoxicity of cephaloridine, cefazolin and mercuric chloride was studied in rabbits of various ages. Cephaloridine produced dose-related elevations in serum urea nitrogen, creatinine and renal tubular necrosis in adult and 30-day-old rabbits, only slight changes at 15 days of age and no effect in 5-day-old rabbits. Cefazolin also produced dose-related nephrotoxicity in adult rabbits but no effect in 15-day-old rabbits. Mercuric chloride administration resulted in similar nephrotoxicity in 5-, 15- and 30-day-old rabbits and adults. The development of susceptibility to cephaloridine nephrotoxicity paralleled the maturation of the renal anionic transport system as determined by the accumulation of p-aminohippurate by renal cortical slices in vitro. Substrate stimulation of the anionic transport system by p-aminohippurate or penicillin increased the nephrotoxicity of cephaloridine in between rabbits. The authors concluded that the lack of cephaloridine nephrotoxicity in newborn rabbits is due to the incomplete development of the renal anionic transport system.     

Evolutionary Algorithms in Drug Design

Designing a drug is the process of finding or creating a molecule which has a specific activity on a biological organism. Drug design is difficult since there are only few molecules that are both effective against a certain disease and exhibit other necessary physiological properties, such as absorption by the body and safety of use. The main problem of drug design is therefore how to explore the chemical space of many possible molecules to find the few suitable ones. Computational methods are increasingly being used for this purpose, among them evolutionary algorithms. This review will focus on the applications of evolutionary algorithms in drug design, in which evolutionary algorithms are used both to create new molecules and to construct methods for predicting the properties of real or yet unexisting molecules. We will also discuss the progress and problems of application of evolutionary algorithms in this field, as well as possible developments and future perspectives.     

Inter-comparison of laser photoacoustic spectroscopy and gas chromatography techniques for measurements of ethene in the atmosphere

Laser photoacoustic spectroscopy (LPAS) is highly suitable for the detection of ethene in air due to the overlap between its strongest absorption lines and the wavelengths accessible by high-powered CO2 lasers. Here, we test the ability of LPAS to measure ethene in ambient air by comparing the measurements in urban air with those from a gas chromatography flame-ionization detection (GC-FID) instrument. Over the course of several days, we obtained quantitative agreement between the two measurements. Over this period, the LPAS instrument had a positive offset of 330 +/- 140 pptv (parts-per-trillion by volume) relative to the GC-FID instrument, possibly caused by interference from other species. The detection limit of the LPAS instrument is currently estimated around 1 ppbv and is limited by this offset and the statistical noise in the data. We conclude that LPAS has the potential to provide fast-response measurements of ethene in the atmosphere, with significant advantages over existing techniques when measuring from moving platforms and in the vicinity of emission sources.     

Analysis of cultured neuronal networks using intraburst firing characteristics

It is an open question whether neuronal networks, cultured on multielectrode arrays, retain any capability to usefully process information (learning and memory). A necessary prerequisite for learning is that stimulation can induce lasting changes in the network. To observe these changes, one needs a method to describe the network in sufficient detail, while stable in normal circumstances. We analyzed the spontaneous bursting activity that is encountered in dissociated cultures of rat neocortical cells. Burst profiles (BPs) were made by estimating the instantaneous array-wide firing frequency. The shape of the BPs was found to be stable on a time scale of hours. Spatiotemporal detail is provided by analyzing the instantaneous firing frequency per electrode. The resulting phase profiles (PPs) were estimated by aligning BPs to their peak spiking rate over a period of 15 min. The PPs reveal a stable spatiotemporal pattern of activity during bursts over a period of several hours, making them useful for plasticity and learning studies. We also show that PPs can be used to estimate conditional firing probabilities. Doing so, yields an approach in which network bursting behavior and functional connectivity can be studied.     

Microbial systems biology: new frontiers open to predictive microbiology

The field of Systems Biology is a rapidly evolving area of research. It follows on from the previous experimental and theoretical 'omics' revolution in biology. Now that we have through the use of these tools many 'indices' of biological systems available the next step is to actually start composing the systems that these indices specify. In this paper we will discuss the developments in the field of Systems Biology as they pertain to predictive food microbiology and give an example of state of the art current approaches. The data discussed in the case study deal with the resistance of the yeast Saccharomyces cerevisiae towards environmental temperature changes through adaptation of its metabolism, protein signalling and gene-expression. The results are integrated and its implications for the definition of new experiments discussed; the iteration between experiment driven model definition and model driven experimentation being characteristic for contemporary Systems Biology approaches. The stress condition discussed represents in no way a practical situation in food microbiology but what it teaches may well be applied in such cases. We will indicate how the latter may be achieved.     

Targeting Inflammation after Myocardial Infarction: A Therapeutic Opportunity for Extracellular Vesicles?

After myocardial infarction (MI), a strong inflammatory response takes place in the heart to remove the dead tissue resulting from ischemic injury. A growing body of evidence suggests that timely resolution of this inflammatory process may aid in the prevention of adverse cardiac remodeling and heart failure post-MI. The present challenge is to find a way to stimulate this process without interfering with the reparative role of the immune system. Extracellular vesicles (EVs) are natural membrane particles that are released by cells and carry different macromolecules, including proteins and non-coding RNAs. In recent years, EVs derived from various stem and progenitor cells have been demonstrated to possess regenerative properties. They can provide cardioprotection via several mechanisms of action, including immunomodulation. In this review, we summarize the role of the innate immune system in post-MI healing. We then discuss the mechanisms by which EVs modulate cardiac inflammation in preclinical models of myocardial injury through regulation of monocyte influx and macrophage function. Finally, we provide suggestions for further optimization of EV-based therapy to improve its potential for the treatment of MI.