On some operations on strings suggested by gene assembly in ciliates

We define three operations on strings and languages suggested by the process of gene assembly in hypotrichous ciliates. This process is considered to be a prine example of DNA computing in vivo. This paper is devoted to some computational aspects of these operations from a formal language point of view. The closure of the classes of regular and context-free languages under these operations is settled. Then, we consider theld-macronuclear language of a given languageL, which consists of allld-macronuclear strings obtained from the strings ofL by iteratively applying the loop-direct repeat-excision. Finally, we discuss some open problems and further directions of research. Rudolf Freund: He received his master and doctor degree in computer science from the Vienna University of Technology, Austria, in 1980 and 1982, respectively. In 1986, he received his master degree in mathematics and physics from the University Vienna, Austria. In 1988 he joined the Vienna University of Technology in Austria, where he became an Associate Professor in September 1995. He has given various lectures in theoretical computer science, especially on formal languages and automata. His research interests include array and graph grammars, regulated rewritung, infinite words, syntactic pattern recognition, neural networks, and especially models and systems for biological computing. In these fields he is author of more than sixty scientific papers. Carlos Martín-Vide: He is Professor and Head of the Research Group on Mathematical Linguistics at Rovira i Virgili University, Tarragona, Spain. His specialities are formal language theory and mathematical linguistics. His last volume edited is Where Mathematics, Computer Science, Linguistics and Biology Meet (Kluwer, 2001, with V. Mitrana). He published 150 papers in conference proceedings and journals such as: Acta Informatica, BioSystems. Computational Linguistics, Computers and Artificial Intelligence, Information Processing Letters, Information Sciences, International Journal of Computer Mathematics, New Generation Computing, Publicationes Mathematicae Debrecen, and Theoretical Computer Science. He is the editor-in-chief of the journal Grammars (Kluwer), and the chairman of the 1st International PhD School in Formal Languages and Applications (2001–2003). Victor Mitrana, Ph.D.: He is Professor of Computer Science at the Faculty of Mathematics, University of Bucharest. He received his MSc and PhD from the University of Bucharest in 1986 and 1993, respectively. In 1999 he was awarded with the “Gheorghe Lazar” Prize for Mathematics of the Romanian Academy. His research interests include: formal language theory and applications, combinatorics on words, computational models inspired from biology, mathematical linguistics. In these areas, he published three books, more than 100 papers, and edited two books. He is an associate editor of “The Korean Journal of Computational and Applied Mathematics” and an editor of “Journal of Universal Computer Science”.     

Prognose der Sorptionskinetik organischer Schadstoffe in heterogenem Aquifermaterial

A model for the simulation of kinetic sorption processes in heterogeneous aquifer material is presented. Sorption kinetics is responsible for the long persistence of many organic contaminants in the subsurface. Therefore, reliable model predictions of these processes are of major importance concerning, for instance, the design of efficient remediation strategies. The modeling approach presented here recognizes sorption kinetics as retarded diffusion within the intra-particle pore space and, in particular, takes into account the sedimentological and petrographical composition of the aquifer material. This is in accordance with results from laboratory experiments quantifying sorption/desorption processes. For solving the model equations a finite-difference scheme is applied which incorporates several features proven to be relevant in practical model applications (mass balance, flexible choice of boundary conditions, easy handling). The simulation results shown here focus on the impact of aquifer heterogeneity (lithological composition, grain size distribution) on sorption and desorption kinetics of organic contaminants. Furthermore, this approach can be straightforwardly coupled to existing software for simulating multi-dimensional solute transport.     

A Local Database Manager for Engineering Analysis Systems

Abstract: A local database manager (LDBM) is presented. It is a software development tool consisting of a set of easy-to-use in-core data management subroutines written in FORTRAN 77. One of the main motivations for the development of this LDBM was to enhance the eflcient use of core memory which seems to be obvious with respect to a PC programming environment. However, even on virtual machines, high performance achieved by minimizing page faults is strongly based on a sophisticated database management system (DBMS). In order to accomplish this objective, the LDBM allows the use of different data types according to the requirements of the actual situation and to the existing programming environment. Integer, short integer, real, double precision, complex, double complex and character data can be handled. Moreover, a two-level hierarchical data structure is used which groups related data in a different and more economic way rather than by means of increasing the number of levels in the DIMENSION statement. Of course, old, no longer used data may be deleted, leaving room for the allocation of new data. Using a technique of 'flexible garbage collection', i.e. the ensuing gap after the deletion of a data block is not automatically closed, the time consumed by the LDBM during a deletion operation is actually not affected by the length of data blocks.     

Membrane-permeant esters of phosphatidylinositol 3,4,5-trisphosphate

Phosphoinositide 3-OH kinases and their products, D-3 phosphorylated phosphoinositides, are increasingly recognized as crucial elements in many signaling cascades. A reliable means to introduce these lipids into intact cells would be of great value for showing the physiological roles of this pathway and for testing the specificity of pharmacological inhibitors of the kinases. We have stereospecifically synthesized di-C8-PIP3/AM and di-C12-PIP3/AM, the heptakis(acetoxymethyl) esters of dioctanoyl- and dilauroylphosphatidylinositol 3,4,5-trisphosphate, in 14 steps from myo-inositol. The ability of these uncharged lipophilic derivatives to deliver phosphatidylinositol 3,4,5-trisphosphate across cell membranes was demonstrated on 3T3-L1 adipocytes and T84 colon carcinoma monolayers. Insulin stimulation of hexose uptake into adipocytes was inhibited by the kinase inhibitor wortmannin and was largely restored by di-C8-PIP3/AM, which had no effect in the absence of insulin. Thus phosphatidylinositol 3,4,5-trisphosphate or a metabolite was necessary but not sufficient for stimulation of hexose transport. In T84 epithelial monolayers, di-C12-PIP3/AM mimicked epidermal growth factor in inhibiting chloride secretion and potassium efflux, suggesting that phosphatidylinositol 3,4, 5-trisphosphate was sufficient to modulate these fluxes and mediate epidermal growth factor's action.     

Die Erhöhung der Grundfrequenz und der Beullast von Kreisplatten durch geeignete plastische Verformung

Zusammenfassung Eine M?glichkeit, ohne Mehraufwand an Material oder Verwendung teurerer Werkstoffe das dynamische Verhalten oder die Tragf?higkeit von Bauteilen zu verbessern, wird am Beispiel der Grundfrequenz- und Beullaststeigerung von Kreisplatten durch das Einpr?gen von geeigneten Eigenspannungszust?nden dargelegt. Die Ergebnisse einer Optimierung solcher Eigenspannungsfelder werden dargestellt, und die M?glichkeit der Erzeugung geeigneter Eigenspannungszust?nde wird an Hand eines Experiments nachgewiesen.     

Experimental activation energies for evolution of oxygen and chlorine on oxide electrodes

The chlorine and oxygen overpotential in dependence on the current density i (A cm^?2) and on the temperature in the range of 15–75°C was measured at γ-MnO₂ and β-PbO₂ electrodes in concentrated water solutions of sodium chloride and perchlorate. From the measured values the experimental activation energy in dependence on overpotential was calculated and, for the temperature of 25°C, the constants of Tafel's equation (a,b) (α, i_o respectively) were evaluated.     

Composition of Chemical Attractants Affects Trap Catches of the Australian Sheep Blowfly, Lucilia cuprina, and Other Blowflies

Numbers of Lucilia cuprina (Australian sheep blowfly), Chrysomya spp., and Calliphora spp. blowflies caught on sticky traps baited with various synthetic attractants or a standard liver/sodium sulfide attractant in western Queensland were recorded. Numbers of each genus collected were influenced by the composition of the chemical attractants. Attractant mixtures based on 2-mercaptoethanol, indole, butanoic/pentanoic acid, and a sodium sulfide solution gave 5- to 20-fold higher L. cuprina catches than the liver standard. These blends attracted similar numbers of Chrysomya spp. (0.85-2.7x) and fewer Calliphora spp. (0.02-0.2x) compared to the liver standard. These synthetic attractants were more effective and selective for L. cuprina than the standard liver/sodium sulfide attractant, and they can be packaged in controlled-release dispensers to generate constant, prolonged release of the attractant.     

Aquatic hypoxia is a teratogen and affects fish embryonic development

Hypoxia occurs over large areas in aquatic systems worldwide, and there is growing concern that hypoxia may affect aquatic animals, leading to population decline and changes in community by elimination of sensitive species. For the first time, we report that sublethal levels of hypoxia can significantly increase (+77.4%) malformation in fish embryonic development. Disruption of apoptotic pattern was clearly evident at 24 h post-fertilization, which may be a major cause of malformation. Furthermore, embryonic development was delayed, and balance of sex hormones (testosterone and estradiol) was disturbed during embryonic stages, implicating that subsequent sexual development may also be affected. Overall, our results imply that hypoxia may have a teratogenic effect on fish and delay fish embryonic development, which may subsequently impair species fitness leading to natural population decline.