Sampled longest common prefix array

When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main building blocks in many compressed suffix tree proposals. In this paper, we describe a new compressed LCP representation: the sampled LCP array. We show that when used with a compressed suffix array (CSA), the sampled LCP array often offers better time/space trade-offs than the existing alternatives. We also show how to construct the compressed representations of the LCP array directly from a CSA

Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences

Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.

FM—index算法性能测试及并行化

介绍了FM-index压缩查询技术，详细阐述了FM—index的工作流程，描述了实现计算字符串在压缩文本中出现次数的算法。对FM-index的源代码在Linux平台上进行了测试，从测试结果分析了使用FM-index进行压缩查询的优点和不足。最后给出了加快FM-index压缩速度的一个并行化算法的初步设计思路。

New modal feed network for a compact monopole array with isolated ports

An element spacing of less than half a wavelength introduces strong mutual coupling between the ports of compact antenna arrays. The strong coupling causes significant system performance degradation. A decoupling network may compensate for the mutual coupling. Alternatively, port decoupling can be achieved using a modal feed network. In response to an input signal at one of the input ports, this feed network excites the antenna elements in accordance with one of the eigenvectors of the array scattering parameter matrix. In this paper, a novel 4-element monopole array is described. The feed network of the array is implemented as a planar ring-type circuit in stripline with four coupled line sections. The new configuration offers a significant reduction in size, resulting in a very compact array.

Microphone array shape calibration in diffuse noise fields

This correspondence presents a microphone array shape calibration procedure for diffuse noise environments. The procedure estimates intermicrophone distances by fitting the measured noise coherence with its theoretical model and then estimates the array geometry using classical multidimensional scaling. The technique is validated on noise recordings from two office environments.

Air vehicle simulator : An application for a cable array robot

The development of autonomous air vehicles can be an expensive research pursuit. To alleviate some of the financial burden of this process, we have constructed a system consisting of four winches each attached to a central pod (the simulated air vehicle) via cables - a cable-array robot. The system is capable of precisely controlling the three dimensional position of the pod allowing effective testing of sensing and control strategies before experimentation on a free-flying vehicle. In this paper, we present a brief overview of the system and provide a practical control strategy for such a system. ©2005 IEEE.

A cable-array robot for air vehicle simulation

The development of autonomous air vehicles can be an expensive research pursuit. To alleviate some of the financial burden of this process, we have constructed a system consisting of four winches each attached to a central pod (the simulated air vehicle) via cables - a cable-array robot. The system is capable of precisely controlling the three dimensional position of the pod allowing effective testing of sensing and control strategies before experimentation on a free-flying vehicle. In this paper, we present a brief overview of the system and provide a practical control strategy for such a system.

Candidate metastasis suppressor genes uncovered by array comparative genomic hybridization in a mouse allograft model of prostate cancer.

Background The purpose of this study was to identify candidate metastasis suppressor genes from a mouse allograft model of prostate cancer (NE-10). This allograft model originally developed metastases by twelve weeks after implantation in male athymic nude mice, but lost the ability to metastasize after a number of in vivo passages. We performed high resolution array comparative genomic hybridization on the metastasizing and non-metastasizing allografts to identify chromosome imbalances that differed between the two groups of tumors. Results This analysis uncovered a deletion on chromosome 2 that differed between the metastasizing and non-metastasizing tumors. Bioinformatics filters were employed to mine this region of the genome for candidate metastasis suppressor genes. Of the 146 known genes that reside within the region of interest on mouse chromosome 2, four candidate metastasis suppressor genes (Slc27a2, Mall, Snrpb, and Rassf2) were identified. Quantitative expression analysis confirmed decreased expression of these genes in the metastasizing compared to non-metastasizing tumors. Conclusion This study presents combined genomics and bioinformatics approaches for identifying potential metastasis suppressor genes. The genes identified here are candidates for further studies to determine their functional role in inhibiting metastases in the NE-10 allograft model and human prostate cancer.