On denoising and compression of DNA microarray images

We address the problems of noise and huge data sizes in microarray images. First, we propose a mixture model for describing the statistical and structural properties of microarray images. Then, based on the microarray image model, we present methods for denoising and for compressing microarray images. The denoising method is based on a variant of the translation-invariant wavelet transform. The compression method introduces the notion of approximate contexts (rather than traditional exact contexts) in modeling the symbol probabilities in a microarray image. This inexact context modeling approach is important in dealing with the noisy nature of microarray images. Using the proposed denoising and compression methods, we describe a near-lossless compression scheme suitable for microarray images. Results on both denoising and compression are included, which show the performance of the proposed methods. Further experiments using the results of the proposed near-lossless compression scheme in gene clustering using cell-cycle microarray data for S. cerevisiae showed a general improvement in the clustering performance, when compared with using the original data. This provides an indirect validation of the effectiveness of the proposed denoising method.     

海洋石油开发工业污染物产生系数和排放系数研究

污染物产生系数和排放系数是工程环境影响评价的重要指标,但对于海洋石油开发工程环境影响评价来说,迄今尚无具权威性的系数可资使用。在我国近海石油开发工程污染源系统调查的基础上,对海洋石油开发行业污染物产生系数和排放系数的定义、计算方法、应用范围及应用方式进行了探讨,研究结果可为海洋石油开发工程项目环境影响评价及环境保护管理,以及行业或企业有关标准的制定提供参考。     

Public grid computing participation: An exploratory study of determinants

Using the Internet, “public” computing grids can be assembled using “volunteered” PCs. To achieve this, volunteers download and install a software application capable of sensing periods of low local processor activity. During such times, this program on the local PC downloads and processes a subset of the project's data. At the completion of processing, the results are uploaded to the project and the cycle repeats.     

Minimum spanning trees made easier via multi-objective optimization

Many real-world problems are multi-objective optimization problems and evolutionary algorithms are quite successful on such problems. Since the task is to compute or approximate the Pareto front, multi-objective optimization problems are considered as more difficult than single-objective problems. One should not forget that the fitness vector with respect to more than one objective contains more information that in principle can direct the search of evolutionary algorithms. Therefore, it is possible that a single-objective problem can be solved more efficiently via a generalized multi-objective model of the problem. That this is indeed the case is proved by investigating the computation of minimum spanning trees.This work was supported by the Deutsche Forschungsgemeinschaft (DFG) as part of the Collaborative Research Center Computational Intelligence (SFB 531) and by the German-Israeli Foundation (GIF) in the project Robustness Aspects of Algorithms.     

The Construction of Minimal DNA Expressions

We describe a formal language/notation for DNA molecules that may contain nicks and gaps. The elements of the language, DNA expressions, denote formal DNA molecules. Different DNA expressions may denote the same formal DNA molecule. We analyse the shortest DNA expressions denoting a given formal DNA molecule. We determine lower bounds on their lengths and explain how we construct these minimal DNA expressions.     

Accumulation of amplified target DNAs using thiol/biotin labeling, S1 nuclease, and ferrocene-streptavidin-magnetic system and a direct detection of specific DNA signals with screen printed gold electrode

Combinations of PCR-based amplification platform using 5′ thiolated and biotinylated specific primers, S1 nuclease-PCR products treatment, ferrocene-streptavidin (Fc-Stv)-magnetic binding for DNA accumulation, and screen printed gold electrode for the DNA allocation, were applied to Hoechst 33258-induced DNA aggregation and signals induction system for direct signals detection and DNA quantification in food samples. Thiolated and biotinylated at each 5′ terminus enabled DNA purification through S1 nuclease treatment for primers and non-specific DNA elimination and enabled DNA trapping with a ferrocene-streptavidin-magnetic system. This facilitated the accumulation of target DNAs at higher concentration, resulting in enhanced signals. After allocation of DNA on the surface of gold electrode via thiol binding, intensity of DNA signals through these treatments could be measured directly after being induced by Hoechst 33258. Wider amplitude changes in anodic current peaks between negative and positive samples (increasing from 3.70 to 10.10 μA) compared with those applied with no treatment combinations (decreasing from 3.92 to 1.23 μA) were observed. This enhancement of the signals allowed a greater efficiency of DNA quantification. When this combination was used for GMOs content estimation in reference samples, results revealed an improved accuracy from 66% to 96%. The combined biosensor system, although more costly than the standard Hoechst 33258/carbon electrode system, provided an alternative choice for DNA quantification, offering labor-free immobilization of probe onto electrode surface, easy test administration, and efficient semi-quantitative test without expensive instruments.     

1D selection of 2D objects in head-worn displays

In current desktop user interfaces, selection is usually accomplished easily with a mouse or a similar two-dimensional locator. In wearable computing, however, controlling two dimensions simultaneously gets significantly harder: a change in one dimension results easily in an undesired change in the other dimension as well when the user is occupied with a parallel task – such as walking. We present a way to overcome this problem by applying one-dimensional selection for graphical user interfaces in head-worn displays. Our new interaction technique allows a wearable computer user to perform object selection tasks easily and accurately. The technique is based on a visible circle on the screen. The user controls the circle, altering its radius with a one-dimensional valuator. The midpoint of the circle is in the middle of the screen. The object currently on the perimeter of the circle is highlighted and can be selected. Our preliminary usability evaluation, applying our custom evaluation method designed especially for walking users, indicates that the proposed technique is usable also when walking.     

网格计算及其应用

网络计算给互联网带来了新的活力，它是一种新型的分布计算技术，致力于解决复杂度很高的新应用问题，文中简述了网格计算的定义、体系结构、关键问题、当前几个有代表性的网格系统以及网格应用实例，并分析了风格计算发展趋势。     

基于质粒的DNA计算模型研究

论文给出了一种基于环状质粒DNA计算的新方法,这种计算质粒包含一个特殊的插入DNA序列片断,每个片断定位在匹配的限制性内切位点,通过剪切和粘贴实现计算过程。论文同时给出了生物计算模型和相关的数学描述,这种模式的计算有待进一步研究。