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Agnese Kokina and Nils Rostoks

-192. Mejlhede, N., Kyjovska, Z., Backes, G., Burhenne, K., Rasmussen, S. K., Jahoor, A. (2006). EcoTILLING for the identification of allelic variation in the powdery mildew resistance genes mlo and Mla of barley. Plant Breeding , 125, 461-467. Rostoks, N., Mudie, S., Cardle, L., Russell, J., Ramsay, L., Booth, A., Svensson, J. T., Wanamaker, S. I., Walia, H., Rodriguez, E. M., Hedley, P. E., Liu, H., Morris, J., Close, T. J., Marshall, D. F., Waugh, R. (2005). Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to

Open access

Ingrida Mazeikiene, Darius Kviklys, Jurate Brone Siksnianiene, Dainius Zinkus and Vidmantas Stanys

Abstract

Prunus necrotic ring spot ilarvirus (PNRSV) and Apple chlorotic leaf spot trichovirus (ACLSV) are common in plum orchards. The aim of the study was to obtain virus-free planting material of Prunus domestica L. by chemotherapy in vitro. Ribavirin at concentrations of 10 to 50 mg·l−1 was added to Murashige–Skoog (MS) nutrition medium for virus eradication from microshoots. After a two-week period of chemotherapy, meristems were subcultured monthly on MS medium and proliferation index of shoots was estimated. Microshoots were retested by reverse transcription polymerase chain reaction for presence of virus. At lowest concentrations of 10 mg·l−1 ribavirin was entirely ineffective for ACLSV and 10 to 30 mg·l−1 was ineffective for PNRSV elimination. Ribavirin concentrations of 40 and 50 mg·l−1 destroyed both pathogens. However, at higher concentrations of 40 and 50 mg·l−1 ribavirin exhibited some signs of phytotoxicity on microshoots in the first sub-cultivation period. In order to test the genetic stability of the microplants after chemotherapy the amplified fragment length polymorphism (AFLP) method was applied. Plant genome stability in ‘Magna Glauca’ at concentrations of 40 mg·l−1 was damaged, as the presence of polymorphic AFLP markers were observed.

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Angelika Voronova and Dainis Ruņģis

–466. Feschotte, C., Jiang, N., Wessler, S. R. (2002). Plant transposable elements: Where genetics meets genomics. Nat. Rev. Genet ., 3 , 329–341. Finnegan, D. J. (1989). Eukaryotic transposable elements and genome evolution. Trends. Genet ., 5 , 103–107. Flavell, A. J., Pearce, S. R., Kumar, A. (1994). Plant transposable elements and the genome. Curr. Opin. Genet. Dev ., 4 , 838–844. Friesen, N., Brandes, A., Heslop-Harrison, J. S. (2001). Diversity, origin and distribution of retrotransposons ( gypsy and copia ) in conifers. Mol. Biol. Evol ., 18 (7), 1176

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Jarosław Smoczek

Abstract

A hybrid method combining an evolutionary search strategy, interval mathematics and pole assignment-based closed-loop control synthesis is proposed to design a robust TSK fuzzy controller. The design objective is to minimize the number of linear controllers associated with rule conclusions and tune the triangular-shaped membership function parameters of a fuzzy controller to satisfy stability and desired dynamic performances in the presence of system parameter variation. The robust performance objective function is derived based on an interval Diophantine equation. Thus, the objective of a fuzzy logic-based control scheme is to place all the closed-loop control system characteristic polynomial coefficients within desired intervals. The reproduction process in the proposed Evolutionary Algorithm (EA) is based on the arithmetical crossover, uniform and non-uniform mutation along with gene deletion/insertion mutation ensuring a diversity of genomes sizes, as well as a diversity in the parameter space of membership functions. The proposed algorithm was implemented to design a fuzzy logic-based anti-sway crane control system taking into consideration the rope length and the mass of a payload variation. The results of experiments conducted using the EA for different conditions assumed for system parameter intervals and desired closed-loop system performances are compared with results achieved using the iterative procedure which is also described in the paper.

Open access

Peter Recht and Eva-Maria Sprengel

References [1] S. Antonakopulos and L. Zhang, Approximation algorithms for grooming in optical network design, Theoret. Comput. Sci. 412 (2011) 3738-3751. doi:10.1016/j.tcs.2011.03.034 [2] F. Bäbler, Über eine spezielle Klasse Euler’scher Graphen, Comment. Math. Helv. 27 (1953) 81-100. doi:10.1007/BF02564555 [3] V. Bafna and P.A. Pevzner, Genome rearrangement and sorting by reversals, SIAM J. Comput. 25 (1996) 272-289. doi:10.1137/S0097539793250627 [4] A. Caprara, Sorting permutations by

Open access

Thomas Lumley

References Anderson, R.A. (2001). Security Engineering. Hoboken, NJ: John Wiley & Sons. Binder, D.A. (1983). On the Variances of Asymptotically Normal Estimators from Complex Surveys. International Statistical Review, 51, 279-292. Church, G., Heeney, C., Hawkins, N., De Vries, J., Boddington, P., Kaye, J., Bobrow, M., and Weir, B. (2009). Public Access to Genome-Wide Data: Five Views on Balancing Research with Privacy and Protection. PLoS Genetics, 5(10), p. e1000665. Estevao, V

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Lakshmanan Kuppusamy and Anand Mahendran

References Boullier, P. and Sagot, B. (2011). Multi-component tree insertion grammars, in P. De Groote et al. (Eds.), Formal Grammar 2009 , Lecture Notes in Artificial Intelligence, Vol. 5591, Springer, Berlin/Heidelberg, pp. 31–46. Brendel, V. and Busse, H.G. (1984). Genome structure described by formal languages, Nucleic Acids Research 12 (5): 2561–2568. Brown, M. and Wilson, C. (1995). RNA pseudoknot modelling using intersections of stochastic context free grammars with applications to database search, Proceedings of the Pacific

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Rafał Biedrzycki and Jarosław Arabas

.G., Worley, K.C., Zhang, L., Milshina, N.V., Jiang, H., Reese, J.T., Childs, K.L., Venkatraman, A., Dickens, C.M., Weinstock, G.M. and Gibbs, R.A. (2006). Community annotation: Procedures, protocols, and supporting tools, Genome Research 16 (11): 1329-1333. Kashiwabara, A.Y., Vieira, D.C.G., Machado-Lima, A. and Durham, A.M. (2007). Splice site prediction using stochastic regular grammars, GMR 6 (1): 105-115. Michalewicz, Z. (1996). Genetic Algorithms + Data Structures = Evolution Programs, 3rd Edn., Springer-Verlag, London

Open access

Allan Bickle

References [1] M. Altaf-Ul-Amin, K. Nishikata, T. Koma, T.Miyasato, Y. Shinbo, M. Arifuzzaman, C. Wada, M. Maeda, et al., Prediction of protein functions based on k-cores of protein-protein interaction networks and amino acid sequences, Genome Informatics 14 (2003) 498-499. [2] J. Alvarez-Hamelin, L. Dall’Asta, A. Barrat, A. Vespignani, k-core decomposition: a tool for the visualization of large scale networks, Adv. Neural Inf. Process. Syst. 18 (2006) 41. [3] G. Bader, C. Hogue, An automated method for finding

Open access

Marek Sikora and Aleksandra Gruca

support and confirmation or support and anti-support, Engineering Applications of Artificial Intelligence   20 (5): 587-600. Carmona-Saez, P., Chagoyen, M., Rodriguez, A., Trelles, O., Carazo, J. and Pascual-Montano, A. (2006). Integrated analysis of gene expression by association rules discovery, BMC Bioinformatics   7 (1): 54. Carmona-Saez, P., Chagoyen, M., Tirado, F., Carazo, J. and Pascual-Montano, A. (2007). Genecodis: A web-based tool for finding significant concurrent annotations in gene lists, Genome