hyo-xtm: a set of hyper-graph operations on xml topic map toward knowledge management

Knowledge management is a critical issue for the next-generation web application, because the next-generation web is becoming a semantic web, a knowledge-intensive network. XML Topic Map (XTM), a new standard, is appearing in this field as one of the structures for the semantic web. It organizes information in a way that can be optimized for navigation. In this paper, a new set of hyper-graph operations on XTM (HyO-XTM) is proposed to manage the distributed knowledge resources.HyO-XTM is based on the XTM hyper-graph model. It is well applied upon XTM to simplify the workload of knowledge management.The application of the XTM hyper-graph operations is demonstrated by the knowledge management system of a consulting firm. HyO-XTM shows the potential to lead the knowledge management to the next-generation web.

Logistic Map耦合格子模型模拟环带

本论文采用Logistic Map耦合格子模型对高聚物中特有的环带球晶进行了模拟，所得到的模拟结果与实验结果吻合较好。同时，研究结果能够对实验制备环带球晶样品提供可靠的理论指导。 首先，我们对Logistic Map耦合格子模型及模型中的两个模拟参量μ和ε进行分析，同时结合实验中各种实验条件对聚合物结晶行为的影响，认为Logistic Map的动力学特征与聚合物结晶行为非常相似，并且参量μ与实验中的结晶温度相关，即随温度的升高而减小，而参量ε与实验中影响扩散的因素有关，即随温度的升高而增大、随分子量的增大而减小，并且随样品厚度的增大而增大。我们对模型的整个参数空间进行计算，得到了可以形成环带球晶形貌的参数范围，通过进一步研究发现环带图案的带宽随参量μ的增大而变窄，随参量ε的增大而变宽。上述研究结果与实验中带宽随实验条件的变化规律是一致的。 在得到环带图案的基础上，我们又进一步计算得到了靶状和螺旋状形貌的参量μ和ε的具体取值范围。通过改变μ和ε的参数取值，模拟了环带球晶形貌由靶状过渡到螺旋状的过程，即靶状图案的环带由外层向内层逐渐断裂成较短的条带结构，所有的条带结构呈现出以空间某处为中心团聚在一起的形貌；随后，这种“团聚”的形貌逐渐消失了，空间中小的条带结构的排列呈无序状态。随着参数的进一步变化，短的条带结构变成较长的带状结构，并且这些带状结构的边缘逐渐发生卷曲，最终形成了螺旋状图案。我们还考察了系统初值和耦合方式对上述图案的影响，结果发现，形成环带球晶的参数范围对系统初值没有明显的依赖性，然而靶状和螺旋状图案的分布受初值的影响较大。此外，发现只有采用交替耦合、并考虑长程耦合作用的Logistic Map耦合格子模型才可以得到环带球晶图案。 为了更好地与实验结果进行对比，我们利用Logistic Map耦合格子模型对二维空间中的几种受限体系进行了模拟。（一）对温度梯度场中的环带球晶进行模拟，发现环带球晶在低温处较易成核，向高温处生长，并且，高温处环带的带宽比低温处宽。（二）对格子宽度受限情况进行了模拟，发现随着受限方向的宽度越来越窄，球晶尺寸逐渐变小，相邻两个环带球晶碰撞产生的界线变短，三个相邻环带球晶所形成的界线的交汇点减少。（三）研究了受限边界上的成核作用对狭长格子中环带球晶的影响，结果发现，随着受限边界上成核点密度的不断增加，其形貌转变分为三个不同阶段：①当成核密度稍有增大时，环带球晶数量增加，直径变小；②继续增大边界成核密度，使得大量晶层从受限边界向格子内生长，导致环带球晶的数量减少，直径也减小；③当成核点增加到一定程度时，整个空间中只有极少数由格子内部成核生长且直径非常小的环带球晶，而占主导地位的是由成核点垂直于受限边界生长出的穿透晶层。这些模拟结果均与实验结果相符合。 我们将Logistic Map耦合映象格子模型发展到三维空间格子中，得到了与环带球晶形貌一致的图案，并且其带宽随模拟参量μ的增大而变窄，随ε的增大而变宽。这一规律性结果与二维正方格子的模拟结果是一致的。这一部分的研究结果还表明，边界条件和格子尺寸对模拟结果有显著的影响，周期性边界条件导致在小体积立方格子中只能得到靶状图案；而当格子尺寸很大时，可以得到螺旋状环带球晶的图案。最后，通过调节垂直于薄膜平面方向上的格子数来研究薄膜厚度对环带图案带宽的影响，发现环带的带宽随厚度的增加而变宽，这与实验中环带球晶的带宽随样品厚度的增加而变大的结论是一致的。

A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers

P>Common carp (Cyprinus carpio) is an important fish for aquaculture, but genomics of this species is still in its infancy. In this study, a linkage map of common carp based on Amplified Fragment Length Polymorphism (AFLP) and microsatellite (SSR) markers has been generated using gynogenetic haploids. Of 926 markers genotyped, 151 (149 AFLPs, two SSRs) were distorted and eliminated from the linkage analyses. A total of 699 AFLP and 20 microsatellite (SSR) markers were assigned to the map, which comprised 64 linkage groups and covered 5506.9 cM Kosambi, with an average interval distance of 7.66 cM Kosambi. The normality tests on interval map distances showed a non-normal marker distribution. Visual inspection of the map distance distribution histogram showed a cluster of interval map distances on the left side of the chart, which suggested the occurrence of AFLP marker clusters. On the other hand, the lack of an obvious cluster on the right side showed that there were a few big gaps which need more markers to bridge. The correlation analysis showed a highly significant relatedness between the length of linkage group and the number of markers, indicating that the AFLP markers in this map were randomly distributed among different linkage groups. This study is helpful for research into the common carp genome and for further studies of genetics and marker-assisted breeding in this species.

Constrain intergalactic medium from the SZ effect map

In this paper, we try to detect the SZ effect in the 2MASS DWT clusters and less bound objects in order to constrain the warm-hot intergalactic medium distribution on large scales by cross-correlation analysis. The results of both observed WMAP and mock SZ effect map indicate that the hot gas distributes from inside as well as outside of the high density regions of galaxy clusters, which is consistent with the results of both observation and hydro simulation. Therefore, the DWT measurement of the cross-correlation would be a powerful tool to probe the missing of baryons in the universe.

A velocity map ion-imaging study on C2H5SH and C3H7SH photodissociation at 243 nm

Photodissociation dynamics Of C2H5SH, i-C-3-H7SH and n-C3H7SH at 243.1 nm were investigated using velocity map ion-imaging method. H-atom photolysis products were detected by a (2 + 1) resonance enhanced ionization scheme. Both the angular distribution and translational energy distribution of the H-atom elimination processes were determined from the ion images of the H-atom products. The experimental results indicate that the H-atom eliminations from these molecules are mainly direct and fast dissociation processes from a repulsive potential energy state. And a more statistical dissociation process that likely occurs oil the ground state via internal conversion has also been observed. Dissociation energies of the S-H bonds are also derived from the H-atom product translational energy distributions. (C) 2002 Elsevier Science B.V. All rights reserved.

Wear mechanism map of uncoated HSS tools during drilling die-cast magnesium alloy

A wear mechanism map of uncoated high-speed steel (HSS) tools was constructed under the conditions of dry-drilling die-cast magnesium alloys. Three wear mechanisms appear in the map based on the microanalysis of drilled HSS tools by SEM, including adhesive wear, abrasive wear and diffusion wear. In the map, there exists a minor wear region which is called "safety zone". This wear mechanism map will be a good reference for choosing suitable drilling parameters when drilling die-cast magnesium alloys.

The study of banded spherulite patterns by coupled logistic map lattice model

Banded spherulite patterns are simulated in two dimensions by means of a coupled logistic map lattice model. Both target pattern and spiral pattern which have been proved to be existent experimentally in banded spherulite are obtained by choosing suitable parameters in the model. The simulation results also indicate that the band spacing is decreased with the increase of parameter mu in the logistic map and increased with the increase of the coupling parameter epsilon, which is quite similar to the results in some experiments. Moreover, the relationship between the parameters and the corresponding patterns is obtained, and the target patterns and spiral patterns are distinguished for a given group of initial values, which may guide the study of banded spherulite.

Robustness and dissipation of mitogen-activated protein kinases signal transduction network: Underlying funneled landscape against stochastic fluctuations

We uncovered the underlying energy landscape of the mitogen-activated protein kinases signal transduction cellular network by exploring the statistical natures of the Brownian dynamical trajectories. We introduce a dimensionless quantity: The robustness ratio of energy gap versus local roughness to measure the global topography of the underlying landscape. A high robustness ratio implies funneled landscape. The landscape is quite robust against environmental fluctuations and variants of the intrinsic chemical reaction rates.

Simulation of Banded Spherulite Patterns by Coupled Logistic Map Lattice Model in Three Dimensions

Banded spherulite patterns are simulated in three dimensions by means of a Coupled Logistic map lattice model. The patterns obtained by numerical calculation are consistent with those in experiments. The simulation results also indicate that the hand spacing is decreased with the increase of parameter mu in the Logistic map and increased with the increase of the coupling parameter e for cube lattices, and increased with the increase of the thickness of the lattice for polymer film, which is quite similar to the results in some experiments. Spiral pattern in three dimensions is also shown in this paper, which helps us understand the form of banded spherulite in polymers.

A preliminary genetic map of Zhikong scallop (Chlamys farreri Jones et Preston 1904)

Zhikong scallop (Chlamys farreri Jones et Preston 1904) is one of the most important aquaculture species in China. The development of a genetic linkage map would provide a powerful tool for the genetic improvement of this species. Amplified fragment length polymorphism (AFLP) is a PCR-based technique that has proven to be powerful in genome fingerprinting and mapping, and population analysis. Genetic maps of C. farreri were constructed using AFLP markers and a full-sib family with 60 progeny. A total of 503 segregating AFLP markers were obtained, with 472 following the Mendelian segregation ratio of 1:1 and 31 markers showing significant (P< 0.05) segregation distortion. The male map contained 166 informative AFLP markers in 23 linkage groups covering 2468 cM. The average distance between markers was 14.9 cM. The female genetic map consisted of 198 markers in 25 linkage groups spanning 3130 cM with an average inter-marker spacing of 15.8 cM. DNA polymorphisms that segregated in a 3:1 ratio as well as the AFLP markers that were heterozygous in both parents were included to construct combined linkage genetic map. Five shared linkage groups, ranging from 61.1 to 162.5 cM, were identified between the male and female maps, covering 431 cM. Amplified fragment length polymorphism markers appeared to be evenly distributed within the linkage groups. Although preliminary, these maps provide a starting point for the mapping of the functional genes and quantitative trait loci in C. farreri.

Genetic linkage map of bay scallop, Argopecten irradians irradians (Lamarck 1819)

The bay scallop (Argopecten irradians irradians Lamarck 1819) has become one of the most important aquaculture species in China. Genetic improvement of cultured bay scallop can benefit greatly from a better understanding of its genome. In this study, we developed amplified fragment length polymorphisms (AFLPs) and simple sequence repeat markers from expressed sequence tags (EST-SSRs) for linkage analysis in bay scallop. Segregation of 390 AFLP and eight SSR markers was analysed in a mapping population of 97 progeny. Of the AFLP markers analysed, 326 segregated in the expected 1:1 Mendelian ratio, while the remaining 74 (or 19.0%) showed significant deviation, with 33 (44.6%) being deficient in heterozygotes (A/a). Among the eight polymorphic EST-SSR loci, one marker (12.5%) was found skewing from its expected Mendelian ratios. Eighteen per cent of the markers segregating from female parent were distorted compared with 21% of the markers segregating from male parent. The female map included 147 markers in 17 linkage groups (LGs) and covered 1892.4 cM of the genome. In the male map, totally 146 AFLP and SSR markers were grouped in 18 LGs spanning 1937.1 cM. The average inter-marker spacing in female and male map was 12.9 and 13.3 cM respectively. The AFLP and SSR markers were distributed evenly throughout the genome except for a few large gaps over 20 cM. Although preliminary, the genetic maps presented here provide a starting point for the mapping of the bay scallop genome.

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.