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Ondřej Soukup simple matrix grammars, generative power, number of components Překladače a gramatiky The concept of simple matrix grammars was introduced and first studied in early seventies. All the achieved results were summarized in a few following studies and the simple matrix grammars start disappearing from the forefront. This work returns to them and aims to correct some generally accepted historical mistakes. In the following studies, the very first definition of simple matrix grammars has slightly evolved to the modern and currently generally accepted form, nevertheless, the validity of the former related results were not revised. However, these modifications have significant influence on the simple matrix grammars.

Despite the existing beliefs that the simple matrix grammars define an infinite hierarchy of languages depending on the number of their components, we show that two components are exactly enough strong and the addition of another component do not increase the generative power. Moreover, we prove that simple matrix grammars with two components are precisely as strong as matrix grammars. Jakub Šoustar parsing, parallel, communicating, pushdown, automata Překladače a gramatiky In this paper we will look at use of parallel communicating pushdown automata systems (PCPA), that communicates their stacks on request, in parsing. We will present some issues that would accompany their use, and also present some possible ways to deal with those issues.

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New implicit transition mapping for pushdown automata, that are used as a components of a PCPA, will be presented. This new property is aimed at dealing with the issues, that are caused by new requirements which a PCPA poses on pushdown automata. Marek Milkovič Unpacking, Decompilation, Retargetable Decompiler, Reverse Engineering, Executable Files, Packing, Malware, Compression Překladače a gramatiky Executable file packing is a process used for compression or protection of these files. The behavior and intent of such packed executable files is difficult or even impossible to analyze. If we want to analyze the original code, we need to detect the used packer and unpack the executable file with a tool called unpacker. This paper describes the methods used for packing and unpacking of the executable files as well as the implementation of an easily and quickly extensible unpacker, which is going to be used in a decompiler developed by AVG Technologies. This unpacker provides the interface for plugins, which extend the set of supported packers.

Unpacking plugins aim at the methods for unpacking without actually running the packed program; thereby providing security measures and targeting the architecture and platform independent unpacking. A newly proposed generic unpacker achieves comparable results with unpackers used in practice and even outpace them in a few aspects. It shows that even static unpacking methods can produce accurate results. Miloš Musil Amino acid substitutions, Phylogenetic analysis, Mutations, Mutation effect prediction Bioinformatika Many genetic mutations are single nucleotide polymorphisms (SNPs).

Significant number of genetic diseases is caused by non-synonymous SNPs manifested as single point mutations on the protein level. The ability to identify deleterious substitutions could be useful for protein engineering to test whether the proposed mutations do not damage protein function same as for targeting disease causing detrimental mutations. However the experimental validation is costly and the need of predictive computation methods has risen. Here we introduce a new in silico predictor based on the principles of phylogenetic analysis and dissimilarity between original and substituting amino acid physico-chemical properties. Developed algorithm was tested on four datasets with 78,650 mutations from 16,256 sequences in total. The predictor yields up to 72% normalized accuracy and in the comparison with the most existing tools, it is substantially less time consuming.