Formal specification and refinement of a safe train control function

Motivated by the design and development challenges of the BART case study, an approach for developing and analyzing a formal model for reactive systems is presented. The approach makes use of a domain specific language for specifying control algorithms able to satisfy competing properties such as safety and optimality. The domain language, called SPC, offers several key abstractions such as the state, the profile, and the constraint to facilitate problem specification. Using a high-level program transformation system such as HATS being developed at the University of Nebraska at Omaha, specifications in this modelling language can be transformed to ML code. The resulting executable specification can be further refined by applying generic transformations to the abstractions provided by the domain language. Problem dependent transformations utilizing the domain specific knowledge and properties may also be applied. The result is a significantly more efficient implementation which can be used for simulation and gaining deeper insight into design decisions and various control policies. The correctness of transformations can be established using a rewrite-rule based induction theorem prover Rewrite Rule Laboratory developed at the University of New Mexico.

一种用户主导的面向领域应用软件开发新方法

提出一种应用软件开发的新方法 ,称为“用户工程”.这是一种基于构件化软件系统结构的用户主导的面向领域的应用软件开发方法 ,强调用户在应用软件开发中的主导作用 ,试图将应用软件的开发过程变成用户详细定义过程 ,而不仅仅是传统的编程过程 .它为越来越多的应用软件开发需求提供了可能有效的一个途径

A shortest path algorithm for moving objects in spatial network databases

One of the most important kinds of queries in Spatial Network Databases (SNDB) to support location-based services (LBS) is the shortest path query. Given an object in a network, e.g. a location of a car on a road network, and a set of objects of interests, e.g. hotels,gas station, and car, the shortest path query returns the shortest path from the query object to interested objects. The studies of shortest path query have two kinds of ways, online processing and preprocessing. The studies of preprocessing suppose that the interest objects are static. This paper proposes a shortest path algorithm with a set of index structures to support the situation of moving objects. This algorithm can transform a dynamic problem to a static problem. In this paper we focus on road networks. However, our algorithms do not use any domain specific information, and therefore can be applied to any network. This algorithm’s complexity is O(klog2 i), and traditional Dijkstra’s complexity is O((i + k)2).

用户主导的面向领域的需求分析方法

如何认识和了解用户并最终让用户在适当的工具和环境的帮助引导下直接参与到需求分析活动中，可能正是解决软件生产过程中一系列问题的突破口。用户可视为对象、角色或智能体，充分发挥其能动性，对于软件需求的正确性、一致性和完整性大有裨益；同时，把软件专业人员从繁琐的需求分析活动中解放出来，可大大缩短软件的开发周期。

特定领域的数据参考模型建模方法研究

针对领域内数据实体变化频繁,复用性低的问题,提出了特定领域数据参考模型的概念,它基于概念模型的形式,对领域内的通用数据模型进行说明和描述,成为领域内应用系统数据建模的基础.给出了领域数据参考模型的体系架构,它对整个模型进行了纵横向的划分以便作为不同程度的复用的基础.在概念模型构建时,提出了数据模型构建步骤,并引入了"维度","维度层次"和"事实"3个数据仓库中的概念,扩充了ER图中的属性定义,为构建稳定可复用的领域实体提供了有效的途径.

学前儿童朴素生物学“理论”的发展——对“生长”认知的实验研究

There is a debate in cognitive development theory on whether cognitive development is general or specific. More and more researchers think that cognitive development is domain specific. People start to investigate preschoolers' native theory of human being's basic knowledge systems. Naive biology is one of the core domains. But there is argument whether there is separate native biological concepts among preschoolers. The research examined preschoolers' cognitive development of naive biological theory on two levels which is "growth" and "aliveness", and it also examined individual difference and factors that lead to the difference. Three studies were designed. Study 1 was to study preschoolers' cognition on growth, which is a basic trait of living things, and whether children can distinguish living and non-living things with the trait and understanding the causality. Study 2 was to investigate preschoolers' distinction between living things and non-living things from an integrated level. Study 3 was to investigate how children make inferences to unfamiliar things with their domain specific knowledge. The results showed the following: 1. Preschoolers gradually developed naive theory of biology on growth level, but their naive theory on integrated level has not developed. 2 Preschoolers' naive theory of biology is not "all or none", 4- and 5-year-old children showed some distinction between living and non-living things to some extent, they use non-intentional reason to explain the cause of growth and their explanation showed coherence. But growth has not been a criteria of ontological distinction of living and non-living things for 4- and 5-year-old children, most 6-year-old children can distinguish between living and non-living things, and these show the developing process of biological cognition. 3. Preschoolers' biological inference is influenced by their domain-specific knowledge, whether they can make inference to new trait of living things depends on whether they have specific knowledge. In the deductive task, children use their knowledge to make inference to unfamiliar things. 4-year-olds use concrete knowledge more often while the 6-year-old use generalized knowledge more frequency. 4. Preschoolers' knowledge grow with age, but individuals' cognitive development speed at different period. Urban and rural educational background affect cognitive performance. As time goes by, the urban-rural knowledge difference to distinguish living and nonliving things reduces. And preschoolers' are at the same developmental stage because the three age groups have similar causal explanation both in quantity and quality. 5. There is intra-individual difference on preschoolers' naive biological cognition. They show different performance on different tasks and domains, and their cognitive development is sequential, they understand growth earlier than they understand "alive", which is an integrated concept. The intra-individual differences decrease with age.

Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria

Cyclic nucleotides (both cAMP and cGMP) play extremely important roles in cyanobacteria, such as regulating heterocyst formation, respiration, or gliding. Catalyzing the formation of cAMP and cGMP from ATP and GTP is a group of functionally important enzymes named adenylate cyclases and guanylate cyclases, respectively. To understand their evolutionary patterns, in this study, we presented a systematic analysis of all the cyclases in cyanobacterial genomes. We found that different cyanobacteria had various numbers of cyclases in view of their remarkable diversities in genome size and physiology. Most of these cyclases exhibited distinct domain architectures, which implies the versatile functions of cyanobacterial cyclases. Mapping the whole set of cyclase domain architectures from diverse prokaryotic organisms to their phylogenetic tree and detailed phylogenetic analysis of cyclase catalytic domains revealed that lineage-specific domain recruitment appeared to be the most prevailing pattern contributing to the great variability of cyanobacterial cyclase domain architectures. However, other scenarios, such as gene duplication, also occurred during the evolution of cyanobacterial cyclases. Sequence divergence seemed to contribute to the origin of putative guanylate cyclases which were found only in cyanobacteria. In conclusion, the comprehensive survey of cyclases in cyanobacteria provides novel insight into their potential evolutionary mechanisms and further functional implications.

Domain decomposition hybrid method for numerical simulation of bluff body flows:theoretical model and application

The discrete vortex method is not capable of precisely predicting the bluff body flow separation and the fine structure of flow field in the vicinity of the body surface. In order to make a theoretical improvement over the method and to reduce the difficulty in finite-difference solution of N-S equations at high Reynolds number, in the present paper, we suggest a new numerical simulation model and a theoretical method for domain decomposition hybrid combination of finite-difference method and vortex method. Specifically, the full flow. field is decomposed into two domains. In the region of O(R) near the body surface (R is the characteristic dimension of body), we use the finite-difference method to solve the N-S equations and in the exterior domain, we take the Lagrange-Euler vortex method. The connection and coupling conditions for flow in the two domains are established. The specific numerical scheme of this theoretical model is given. As a preliminary application, some numerical simulations for flows at Re=100 and Re-1000 about a circular cylinder are made, and compared with the finite-difference solution of N-S equations for full flow field and experimental results, and the stability of the solution against the change of the interface between the two domains is examined. The results show that the method of the present paper has the advantage of finite-difference solution for N-S equations in precisely predicting the fine structure of flow field, as well as the advantage of vortex method in efficiently computing the global characteristics of the separated flow. It saves computer time and reduces the amount of computation, as compared with pure N-S equation solution. The present method can be used for numerical simulation of bluff body flow at high Reynolds number and would exhibit even greater merit in that case.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Identification of a novel C2 domain factor in ovaries of orange-spotted grouper (Epinephelus coioides)

Follicle consists of an oocyte and a lot of surrounding follicular cells, and significant interactions exist between the oocyte and the somatic cells. In this study, a novel cDNA has been screened from a subtractive cDNA library between tail bud embryos and blastula embryos in the protogynous hermaphrodite orange-spotted grouper (Epinephelus coioides). Its full-length cDNA is 821 bp, and has an ORF of 414 by for encoding a peptide of 137 aa, which shows 38%, 37%, 33%, and 33% homology with 4 putative proteins screened from zebrafish (Danio rerio). Conserved domain search in NCBI reveals a single C2 domain existing in the C2 domain superfamily proteins, and has only 7 beta strands in comparison with 8 beta strands of C2 domains in other C2 domain superfamily proteins. Artificial sex reversal, RT-PCR analysis and Western blot detection demonstrated ovary-specific expression of the C2 domain factor, and therefore the novel gene was designated as E. coioides ovary-specific C2 domain factor, EcOC2 factor. Moreover, predominant expression of EcOC2 factor was further revealed in grouper mature ovary, and its strong immunofluorescence signals were located between granulosa cells and oocyte zona radiata in grouper mature follicles. The data indicate that the novel EcOC2 factor might be a main component that associates between granulosa cells and the oocyte during oocyte maturation, and might play significant roles in regulating oocyte maturation and ovulation. Further studies on its developmental behaviour and physiological functions will elucidate the interactions between oocyte and the surrounding somatic cells and the underlying molecular mechanisms. (C) 2005 Elsevier Inc. All rights reserved.

Zebraflsh z-otu, a novel Otu and Tudor domain-containing gene, is expressed in early stages of oogenesis and embryogenesis

Several studies have suggested that Otu domain had de-ubiquitinating activity and Tudor domain was important for the formation of germ cells. Here, we reported a novel zebrafish ovary-specific gene containing Otu and Tudor domain, z-otu, which was expressed at stages I-III oocytes and embryonic stages from zygotes to early blastula during embryonic cells maintained their totipotency. Therefore, z-otu might link the ubiquitin signaling pathway to early oogenesis and maintaining the totipotency of embryonic cell. (c) 2005 Elsevier B.V. All rights reserved.

PURIFICATION AND CHARACTERIZATION OF A KINASE SPECIFIC FOR THE SERINE-RICH AND ARGININE-RICH PRE-MESSENGER-RNA SPLICING FACTORS

Members of the SR family of pre-mRNA splicing factors are phosphoproteins that share a phosphoepitope specifically recognized by monoclonal antibody (mAb) 104. Recent studies have indicated that phosphorylation may regulate the activity and the intracellular localization of these splicing factors. Here, we report the purification and kinetic properties of SR protein kinase 1 (SRPK1), a kinase specific for SR family members. We demonstrate that the kinase specifically recognizes the SR domain, which contains serine/arginine repeats. Previous studies have shown that dephosphorylated SR proteins did not react with mAb 104 and migrated faster in SDS gels than SR proteins from mammalian cells. We show that SRPK1 restores both mobility and mAB 104 reactivity to a SR protein SF2/ASF (splicing factor 2/alternative splicing factor) produced in bacteria, suggesting that SRPK1 is responsible for the generation of the mAb 104-specific phosphoepitope in vivo. Finally, we have correlated the effects of mutagenesis in the SR domain of SF2/ASF on splicing with those on phosphorylation of the protein by SRPK1, suggesting that phosphorylation of SR proteins is required for splicing.

Design and Verification of the Programming Circuit in an Application-Specific FPGA

In this paper we present a methodology and its implementation for the design and verification of programming circuit used in a family of application-specific FPGAs that share a common architecture. Each member of the family is different either in the types of functional blocks contained or in the number of blocks of each type. The parametrized design methodology is presented here to achieve this goal. Even though our focus is on the programming circuitry that provides the interface between the FPGA core circuit and the external programming hardware, the parametrized design method can be generalized to the design of entire chip for all members in the FPGA family. The method presented here covers the generation of the design RTL files and the support files for synthesis, place-and-route layout and simulations. The proposed method is proven to work smoothly within the complete chip design methodology. We will describe the implementation of this method to the design of the programming circuit in details including the design flow from the behavioral-level design to the final layout as well as the verification. Different package options and different programming modes are included in the description of the design. The circuit design implementation is based on SMIC 0.13-micron CMOS technology.