2083522
Conservation analysis of small RNA genes in Escherichia coli
MOTIVATION
Small RNA (sRNA) genes in Escherichia coli have been in focus recently, as 44 out of 55 experimentally confirmed sRNA genes have been precisely located in the genome. The object of this study is to analyze quantitatively the conservation of these sRNA genes and compare it with the conservation of protein-encoding genes, function-unknown regions and tRNA genes.


RESULTS
The results show that within an evolutionary distance of 0.26, both sRNA genes and protein-encoding genes display a similar tendency in their degrees of conservation at the nucleotide level. In addition, the conservation of sRNA genes is much stronger than function-unknown regions, but much weaker than tRNA genes. Based on the conservation of studied sRNA genes, we also give clues to estimate the total number of sRNA genes in E.coli.


SUPPLEMENTARY INFORMATION
Supplementary information is available at http://www.bioinfo.org.cn/SM/sRNAconservation.htm
18768668
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis
BackgroundAs phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective.ResultsWe reconstructed phylophenetic trees for all available metabolic pathways based on topological similarities, and compared them to the corresponding 16S rRNA-based trees. Similarity values for each pair of trees ranged from 0.044 to 0.297. Using the quartet method, single pathways trees were merged into a comprehensive tree containing information from a large part of the entire metabolic networks. This tree showed considerably higher similarity (0.386) to the corresponding 16S rRNA-based tree than any tree based on a single pathway, but was, on the other hand, sufficiently distinct to preserve unique phylogenetic information not reflected by the 16S rRNA tree.ConclusionWe observed that the topology of different metabolic pathways provided different phylogenetic and phenetic information, depicting the compromise between phylogenetic information and varying evolutionary pressures forming metabolic pathway topologies in different organisms. The phylogenetic information content of the comprehensive tree is substantially higher than that of any tree based on a single pathway, which also gave clues to constraints working on the topology of the global metabolic networks, information that is only partly reflected by the topologies of individual metabolic pathways.
4792658
Active Page Generation via Customizing XML for Data Beans in E-Commerce Applications
In this paper, we analyze enabling technologies for typical e-business applications in terms of their multi-tier system architecture and their Model-Control-View (MCV) programming model. Based on observed limitations of the JSP (Java Server Page) technique commonly adopted for dynamic page generation (the view logic), we instead propose an alternative solution approach, namely, a generic schema mapping strategy to generate XML documents and DTDs from enterprise data beans. First, we describe in detail the XML generation process for the content composition logic. We also outline the XSL processing for the transformation logic. The separation of these two logics results in a generic solution to the bean viewing problem. In particular, it improves the bean reusability via its XML representative compared to the rigid strategy of hard-coding logics into JSP. Our proposed XML mapping solution represents a potentially valuable addition to future versions of the enterprise data beans specification. The trade-off between performance and flexibility of these alternative solutions is discussed. Lastly, we survey the state-of-art research results and emerging stardards related to this XML model mapping approach.
205001001
The Towers of Hanoi Problem with Parallel Moves
Abstract This paper proposes a variant of the towers of Hanoi problem allowing parallel moves. An algorithm for this problem is presented and proved to be optimal.
33569110
A Branch-and-Bound Algorithm for Single-Row Routing
33647867
Manipulating multiple stacks with ordered-heap
Abstract A new method for manipulating multiple stacks based on dynamic data structure is proposed in this paper. A simple data structure called ordered-heap is developed, in which nodes are preserved as a heap, and kept inorder traversal sequence remains unchanged. By employing ordered-heap to a multiple-stacks environment, it is easy and efficient to simultaneously handle several variable-size stacks in a sequential memory area. Our experiments show that not only the total number of item movements in the proposed method is much smaller than in the previous methods, but also the overhead for maintaining data structure in the proposed method is kept within a reasonable range.
6760399
On fixed input distributions for noncoherent communication over high-SNR Rayleigh-fading channels
It is well known that independent and identically distributed Gaussian inputs, scaled appropriately based on the signal-to-noise ratio (SNR), achieve capacity on the additive white Gaussian noise (AWGN) channel at all values of SNR. In this correspondence, we consider the question of whether such good input distributions exist for frequency-nonselective Rayleigh-fading channels, assuming that neither the transmitter nor the receiver has a priori knowledge of the fading coefficients. In this noncoherent regime, for a Gauss-Markov model of the fading channel, we obtain explicit mutual information bounds for the Gaussian input distribution. The fact that Gaussian input generates bounded mutual information motivates the search for better choices of fixed input distributions for high-rate transmission over rapidly varying channels. Necessary and sufficient conditions are derived for characterizing such distributions for the worst case scenario of memoryless fading, using the criterion that the mutual information is unbounded as the SNR gets large. Examples of both discrete and continuous distributions that satisfy these conditions are given. A family of fixed input distributions with mutual information growth rate of O((loglogSNR)/sup 1-u/), u>0 are constructed. It is also proved that there does not exist a single fixed-input distribution that achieves the optimal mutual information growth rate of loglogSNR.