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Better Filtering with Gapped q-Grams

100%

Burkhardt S. , Kärkkäinen J.

Fundamenta Informaticae

2003

tom Vol. 56, nr 1,2

51-70

A popular and well-studied class of filters for approximate string matching compares substrings of length q, the q-grams, in the pattern and the text to identify text areas that contain potential matches. A generalization of the method that uses gapped q-grams instead of contiguous substrings is mentioned a few times in literature but has never been analyzed in any depth. In this paper, we report the first results of a study on gapped q-grams. We show that gapped q-grams can provide orders of magnitude faster and/or more efficient filtering than contiguous q-grams. To achieve these results the arrangement of the gaps in the q-gram and a filter parameter called threshold have to be optimized. Both of these tasks are nontrivial combinatorial optimization problems for which we present efficient solutions. We concentrate on the k mismatches problem, i.e, approximate string matching with the Hamming distance.

The FORMIN 2 protein is required for the remodeling of consolidated memories

51%

Sananbenesi F. , Pinhero P. , Rebola N. , Kerimoglu C. , Burkhardt S. , Rizzoli S. , Mulle C. , Fischer A.

Acta Neurobiologiae Experimentalis

2011

tom 71

nr S

The brain has a remarkable capacity to undergo plasticity changes that are believed to underlie the acquisition, consolidation and maintenance of memory traces. To identify the molecular and cellular substrates of cognitive function is a major aim of modern neuroscience. A critical mechanism that has been implicated with neuronal plasticity is the regulation of the actin cytoskeleton. Thus, we study the role of FORMIN 2 (FMN2), a protein that regulates actin dynamics, in the adult brain of mice. Fmn2-/- mice can normally form hippocampus-dependent associative and spatial memories but display a severe failure in adapting a once acquired memory. Thus, Fmn2-/- mice show dramatic impairments in reversal learning paradigms. On the molecular and cellular levels this phenotype is explained by deregulated actin dynamics in the hippocampal striatum lucidum linked to a reduced number of synaptic vesicles per active zone and led to specific changes in the physiology of mossy fiber-CA3 synapses. Our data indicates that FMN2 at the mossy fiber-CA3 synapse is required for the fine-tuning of hippocampal memory traces.