同步数据流可视化建模和调度优化的实现与研究

数据流是为解决数字信号处理领域应用程序设计、开发难度大等问题而提出的，和传统的控制流相比，数据流能够更加自然地描述信号处理系统，更加清晰地表达系统的并发性。应用数据流设计的信号处理系统具有较高的性能，采用数据流语言能够大大加速DSP应用程序的设计和开发。同步数据流（Synchronous Data Flow，简称SDF）基于数据流，它和数据流最大的不同在于：SDF的计算单元在编译时刻消耗数据和产生数据的数目固定，这一特点决定了采用SDF设计和建立的模型能够在编译时刻确定调度序列，使得SDF适合用于多速率信号处理系统的建模。模型化多处理器系统Modex是一个面向同步数据流的可视化建模系统，它支持开发人员运用SDF进行可视化建模、为建立的模型生成调度序列、对调度序列进行空间优化、为建立的模型生成面向目标平台的C语言代码、对模型仿真验证、对模型进行资源消耗评估、将模型映射到指定的处理器执行等。 本文介绍Modex系统的两个关键技术：可视化建模和SDF调度序列空间优化的实现和研究。文章着重介绍SDF模型描述语言的定义，图元的构建和组织，图元的图形显示，控制图元的控制器，直接操作图元的命令对象，图元和视图之间的同步机制以及图形编辑器等部分的设计和实现。Modex系统的可视化建模基于GEF(Graphical Editing Framework)，为同步数据流建模提供了丰富的可视化编辑操作，同时图元和视图之间松散耦合，可视化建模具有良好的互操作性以及扩展性。文章针对调度序列的空间优化提出了将SAS(Single Appearance Sequence）和非SAS类型调度序列相结合的思想，并基于该思想设计了生成空间优化的非SAS类型调度序列算法IAO（Increase Available Output），并结合EA(Evolutionary Approach)算法实现了面向通用,特别是存在反馈环的SDF模型的空间优化方案SGUTS（Solution for General Graph Using Two Kinds of Sequences）。SGUTS是一个层次化的优化框架，它通过聚集将一个存在反馈的模型分为上层模型和下层模型，然后采用EA、IAO算法分别为这两层模型进行优化，从而得到整个模型的优化结果。SGUTS不仅解决了存在反馈环的SDF模型空间优化问题，而且相比较其他算法，SGUTS取得了较好的优化结果。

PHYLOGENY OF THE SLOW LORISES (GENUS NYCTICEBUS) - AN APPROACH USING MITOCHONDRIAL-DNA RESTRICTION ENZYME ANALYSIS

Mitochondrial DNA polymorphisms in 15 specimens of three species of slow lorises-Nycticebus coucang, N. intermedius, and N. pygmaeus-were analyzed in order to study the evolutionary relationships among the species. Eight restriction types were observed in the samples. Phylogenetic trees constructed on the basis of genetic distances showed that the slow lorises sort into two clusters: four types of N. coucang and three types of N. intermedius plus one type of N. pygmaeus. Our results suggest that there are two valid species in the genus Nycticebus-N. coucang and N. pygmaeus-and that N. intermedius should be included within N. pygmaeus. Divergence between the two species may have begun 2.7 Ma (million years ago). Evolution of gross morphology, chromosomes, and mitochondrial DNA in the slow lorises appears to be concordant.

Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach

Several recent molecular phylogenetic studies of the sisorid catfishes (Sisoridae) have challenged some aspects of their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within this family in these studies highlights the need for additional data and analyses. Here we subjected 15 taxa representing 12 sisorids genera to comprehensive phylogenetic analyses using the second intron of low-copy nuclear S7 ribosomal protein (rpS7) gene and the mitochondrial 16S rRNA gene segments both individually and in combination. The competing sisorid topologies were then tested by using the approximately unbiased (AU) test and the Shimodaira-Hasegawa (SH) test. Our results support previously suggested polyphyly of Pareuchiloglanis. The genus Pseudecheneis is likely to be nested in the glyptosternoids and Glaridoglanis might be basal to the tribe Glyptosternini. However, justified by AU and SH test, the sister-group relationship between Pseudecheneis and the monophyletic glyptosternoids cannot be rejected based on the second intron of rpS7 gene and combined data analyses. It follows that both gene segments are not suitable for resolving the phylogenetic relationships within the sisorid catfishes. Overall, the second intron of rpS7 gene yielded poor phylogenetic performance when compared to 16S rRNA gene, the evolutionary hypothesis of which virtually agreed with the combined data analyses tree. This phenomenon can be explained by the insufficient length and fast saturation of substitutions in the second intron of rpS7 gene, due to substitution patterns such as frequent indels (insertion/deletion events) of bases in the sequences during the evolution.

Molecular cloning, characterization and evolutionary analysis of phytoene desaturase (PDS) gene from Haematococcus pluvialis

Phytoene desaturase is one of the most important enzymes necessary for the biosynthesis of carotenoids in some cyanobacteria, green algae and plants. In this study, genomic DNA and cDNA of pds were cloned from unicellular green alga Haematococcus pluvialis strain323 using PCR and RT-PCR methods. The cDNA was cloned into plasmid pET-28a and efficiently expressed in Escherichia coli BL21. The complete genomic PDS gene of H. pluvialis, 3.3 kb in size, included eight exons and seven introns. To locate transcriptional regulation elements, an approximate 1 kb of 5'-flanking region was isolated by genome-walking method. Results of bioinformatic analysis showed several putative cis-elements e.g. the ABRE motif (abscisic acid responsive element), the C-repeat/DRE (dehydration responsive element) motif and the GCN4 motif were located in 5'-flanking region of pds. Results of phylogenetic analyses reveal that different sources of PDS genes form a separate clade, respectively, with 100% bootstrap support. Moreover, a maximum likelihood approach was employed to detect evidence of positive selection in the evolution of PDS genes. Results of branch-site model analysis suggest that 7.9% of sites along the green algal branch are under positive selection, and the PDS gene in green algae exhibits a different evolutionary pattern from its counterparts in cyanobacteria and plants.