2484888
Search for evolution-related-oligonucleotides and conservative words in rRNA sequences
We describe a method for finding unmapped conserved words in rRNA sequences that is effective, utilizes evolutionary information and does not depend on multiple sequence alignment. Evolutionary distance (called n-distance) between a pair of 16S or 18S rRNA sequences is defined in terms of the difference in the two sets of frequencies of occurrence of oligonucleotides n bases long (n-mers) given by the sequences. These n-distances are used to reconstruct phylogenetic trees for 35 representative organisms from all three kingdoms. The quality of the tree generally improves with increasing n and reaches a plateau of best fit at n=7 or 8. Hence the 7-mer or 8-mer (oligonucleotide of 7 or 8 bases) frequencies provide a basis to describe rRNA evolution. Based on the analysis of the contribution of a particular 7-mers to 7-distances, a set of 612 7-mers (called evolution-related-oligonucleotides, EROs) that are critical to the topology of the best phylogenetic tree are identified. Expanding from this set of EROs, evolution-related conservative words longer than 7 bases in 16S rRNA sequences from an enlarged set of 98 organisms in bacteria and archaea are identified based on two criteria: 1) the word is highly conserved in nearly all species of a kingdom (or a sub-kingdom); and 2) the word is located at nearly the same site in each sequence. Three examples of words thus found are: the 13-mer ggattagataccc located at the end of a loop near H24 (in E.coli) is conservative in almost all species in archaea and bacteria. The 8-mer aacgagcg located on H35 is also conservative in archaea and bacteria. Its expansion, the 32-mer tgttgggttaagtcccgcaacgagcgcaaccc, is conservative in bacteria but not in archaea.
30584838
Shannon Information in Complete Genomes
Shannon information in the genomes of all completely sequenced prokaryotes and eukaryotes are measured in word lengths of two to ten letters. It is found that in a scale-dependent way, the Shannon information in complete genomes are much greater than that in matching random sequences - thousands of times greater in the case of short words. Furthermore, with the exception of the 14 chromosomes of Plasmodium falciparum, the Shannon information in all available complete genomes belong to a universality class given by an extremely simple formula. The data are consistent with a model for genome growth composed of two main ingredients: random segmental duplications that increase the Shannon information in a scale-independent way, and random point mutations that preferentially reduces the larger-scale Shannon information. The inference drawn from the present study is that the large-scale and coarse-grained growth of genomes was selectively neutral and this suggests an independent corroboration of Kimura's neutral theory of evolution.
2331504
Centroidal Voronoi Tessellation-Based Reduced-Order Modeling of Complex Systems
\noindent A reduced-order modeling methodology based on centroidal Voronoi tessellations (CVTs) is introduced. CVTs are special Voronoi tessellations for which the generators of the Voronoi diagram are also the centers of mass (means) of the corresponding Voronoi cells. For discrete data sets, CVTs are closely related to the h-means and k-means clustering techniques. A discussion of reduced-order modeling for complex systems such as fluid flows is given to provide a context for the application of reduced-order bases. Then, detailed descriptions of CVT-based reduced-order bases and how they can be constructed from snapshot sets and how they can be applied to the low-cost simulation of complex systems are given. Subsequently, some concrete incompressible flow examples are used to illustrate the construction and use of CVT-based reduced-order bases. The CVT-based reduced-order modeling methodology is shown to be effective for these examples.
8279890
Location tracking using quorums in mobile ad hoc networks
Abstract We explore applications of quorum systems to the problem of tracking locations of mobile users in mobile ad hoc networks (MANETs). The location tracking system uses biquorum systems, a generalization of traditional quorum systems. We performed extensive simulations of the location tracking system. The simulation results show that our strict biquorum implementation has better performance than the traditional strict quorum implementations. Moreover, our results show that randomized dynamic quorum implementations have better overall performance than strict (bi)quorum implementations.
5288834
Collaborative video searching on a tabletop
Almost all system and application design for multimedia systems is based around a single user working in isolation to perform some task yet much of the work for which we use computers to help us, is based on working collaboratively with colleagues. Groupware systems do support user collaboration but typically this is supported through software and users still physically work independently. Tabletop systems, such as the DiamondTouch from MERL, are interface devices which support direct user collaboration on a tabletop. When a tabletop is used as the interface for a multimedia system, such as a video search system, then this kind of direct collaboration raises many questions for system design. In this paper we present a tabletop system for supporting a pair of users in a video search task and we evaluate the system not only in terms of search performance but also in terms of user–user interaction and how different user personalities within each pair of searchers impacts search performance and user interaction. Incorporating the user into the system evaluation as we have done here reveals several interesting results and has important ramifications for the design of a multimedia search system.
7244802
Design, implementation and testing of an interactive video retrieval system
In this paper we present and discuss the system we developed for the search task of the TRECVID 2002, and its evaluation in an interactive search task. To do this we will look at the strategy we used in designing the system, and we discuss and evaluate the experiments used to determine the value and effectiveness of one system incorporating both feature evidence and transcript retrieval compared to a transcript-only retrieval system. Both systems tested are built on the foundation of the Físchlár System developed and running for a number of years at the CDVP. The system is fully MPEG-7 compliant and uses XML for exchange of information within the overall architecture.
5988668
Using text search for personal photo collections with the MediAssist system
The MediAssist system enables organisation and searching of personal digital photo collections based on contextual information, content-based analysis and semi-automatic annotation. One mode of user interaction uses automatically extracted features to create text surrogates for photos, which enables text search of photo collections without manual annotation. Our evaluation shows that this text search facility is effective for known-item search.