In vitro recombination of homologous genes (family shuffling) has been proposed as an effective search strategy for laboratory evolution of genes and proteins. Few data are available, however, on the composition of shuffled gene libraries, from which one could assess the efficiency of recombination and optimize protocols. Here, probe hybridization is used in a macroarray format to analyze chime...

This study proposes the segmentation procedure of univariate time series based on Fisher’s exact test. We show that an adequate change point can be detected as the minimum value of p-value. It is shown that the proposed procedure can detect change points for an artificial time series. We apply the proposed method to find segments of the foreign exchange rates recursively. It is also applied to ...

We examined whether the perception of the colorfulness of an image is influenced by the adaptation of the visual system to natural and shuffled images with different degrees of saturation. In the experiment, observers first became adapted to several images with different levels of saturation and then their colorfulness perception of a test image was measured. The results show that their percept...

SUMMARY Assessing the statistical significance of structured RNA predicted from multiple sequence alignments relies on the existence of a good null model. We present here a random shuffling algorithm, Multiperm, that preserves not only the gap and local conservation structure in alignments of arbitrarily many sequences, but also the approximate dinucleotide frequencies. No shuffling algorithm t...

Trichoderma reesei can be considered as a candidate for consolidated bioprocessing (CBP) microorganism. However, its ethanol yield needs to be improved significantly. Here the ethanol production of T. reesei CICC 40360 was improved by genome shuffling while simultaneously enhancing the ethanol resistance. The initial mutant population was generated by nitrosoguanidine treatment of the spores, a...

rainfall-runoff modeling is most important component in the water resource management of river basins. the successful application of a conceptual rainfall-runoff model depends on how well it is calibrated. the degree of difficulty in solving the global optimization method is generally dependent on the dimensionality of the model and certain of the characteristics of object function. the purpose...

Resampling techniques such as bagging are often used in supervised learning to produce more accurate classifiers. In this work, we show that multiple-instance learning admits a different form of resampling, which we call “shuffling.” In shuffling, we resample instances in such a way that the resulting bags are likely to be correctly labeled. We show that resampling results in both a reduction o...

Protein structure analysis is one of the most important research issues in the post-genomic era, and faster and more accurate index data structures for such 3-D structures are highly desired for research on proteins. The geometric suffix tree is a very sophisticated index structure that enables fast and accurate search on protein 3-D structures. By using it, we can search from 3-D structure dat...

We use three prevalent scoring methods to test the object-map hypothesis, since validity of this model boils down to fair model comparison with bottom-up saliency models. Please see Appendix B for explanation of state-of-the-art saliency models used here. We report results using the previously proposed Normalized Scanpath Saliency (NSS) (Peters et al., 2005; Parkhurst et al., 2002), Correlation...