Isolation and mapping of telomeric pentanucleotide (TAACC)(n) repeats of the pacific whiteleg shrimp, Penaeus vannamei, using fluorescence in situ hybridization

To develop genetic and physical maps for shrimp, accurate information on the actual number of chromosomes and a large number of genetic markers is needed. Previous reports have shown two different chromosome numbers for the Pacific whiteleg shrimp, Penaeus vannamei, the most important penaeid shrimp species cultured in the Western hemisphere. Preliminary results obtained by direct sequencing of clones from a Sau3A-digested genomic library of P. vannamei ovary identified a large number of (TAACC/GGTTA)-containing SSRs. The objectives of this study were to (1) examine the frequency of (TAACC)(n) repeats in 662 P. vannamei genomic clones that were directly sequenced, and perform homology searches of these clones, (2) confirm the number of chromosomes in testis of P. vannamei, and (3) localize the TAACC repeats in P. vannamei chromosome spreads using fluorescence in situ hybridization (FISH). Results for objective I showed that 395 out of the 662 clones sequenced contained single or multiple SSRs with three or more repeat motifs, 199 of which contained variable tandem repeats of the pentanucleotide (TAACC/GGTTA),, with 3 to 14 copies per sequence. The frequency of (TAACC)n repeats in P. vannamei is 4.68 kb for SSRs with five or more repeat motifs. Sequence comparisons using the BLASTN nonredundant and expressed sequence tag (EST) databases indicated that most of the TAACC-containing clones were similar to either the core pentanucleotide repeat in PVPENTREP locus (GenBank accession no. X82619) or portions of 28S rRNA. Transposable elements (transposase for Tn1000 and reverse transcriptase family members), hypothetical or unnamed protein products, and genes of known function such as 18S and 28S rRNAs, heat shock protein 70, and thrombospondin were identified in non-TAACC-containing clones. For objective 2, the meiotic chromosome number of P. vannamei was confirmed as N = 44. For objective 3, four FISH probes (P1 to P4) containing different numbers of TAACC repeats produced positive signals on telomeres of P. vannamei chromosomes. A few chromosomes had positive signals interstitially. Probe signal strength and chromosome coverage differed in the general order of P1 > P2 > P3 > P4, which correlated with the length of TAACC repeats within the probes: 83, 66, 35, and 30 bp, respectively, suggesting that the TAACC repeats, and not the flanking sequences, produced the TAACC signals at chromosome ends and TAACC is likely the telomere sequence for P. vannamei.

PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.

Characterization and mapping of expressed sequence tags isolated from a subtracted cDNA library of Litopenaeus vannamei injected with white spot syndrome virus

A large number of polymorphic simple sequence repeats (SSRs) or microsatellites are needed to develop a genetic map for shrimp. However, developing an SSR map is very time-consuming, expensive, and most SSRs are not specifically linked to gene loci of immediate interest. We report here on our strategy to develop polymorphic markers using expressed sequence tags (ESTs) by designing primers flanking single or multiple SSRs with three or more repeats. A subtracted cDNA library was prepared using RNA from specific pathogen-free (SPF) Litopenaeus vannamei juveniles (similar to 1 g) collected before (0) and after (48 h) inoculation with the China isolate of white spot syndrome virus (WSSV). A total of 224 clones were sequenced, 194 of which were useful for homology comparisons against annotated genes in NCBI nonredundant (nr) and protein databases, providing 179 sequences encoded by nuclear DNA, 4 mitochondrial DNA, and 11 were similar to portions of WSSV genome. The nuclear sequences clustered in 43 groups, 11 of which were homologous to various ESTs of unknown function, 4 had no homology to any sequence, and 28 showed similarities to known genes of invertebrates and vertebrates, representatives of cellular metabolic processes such as calcium ion balance, cytoskeleton mRNAs, and protein synthesis. A few sequences were homologous to immune system-related (allergens) genes and two were similar to motifs of the sex-lethal gene of Drosophila. A large number of EST sequences were similar to domains of the EF-hand superfamily (Ca2+ binding motif and FRQ protein domain of myosin light chains). Single or multiple SSRs with three or more repeats were found in approximately 61 % of the 179 nuclear sequences. Primer sets were designed from 28 sequences representing 19 known or putative genes and tested for polymorphism (EST-SSR marker) in a small test panel containing 16 individuals. Ten (53%) of the 19 putative or unknown function genes were polymorphic, 4 monomorphic, and 3 either failed to satisfactorily amplify genomic DNA or the allele amplification conditions need to be further optimized. Five polymorphic ESTs were genotyped with the entire reference mapping family, two of them (actin, accession #CX535973 and shrimp allergen arginine kinase, accession #CX535999) did not amplify with all offspring of the IRMF panel suggesting presence of null alleles, and three of them amplified in most of the IRM F offspring and were used for linkage analysis. EF-hand motif of myosin light chain (accession #CX535935) was placed in ShrimpMap's linkage group 7, whereas ribosomal protein S5 (accession #CX535957) and troponin I (accession #CX535976) remained unassigned. Results indicate that (a) a large number of ESTs isolated from this cDNA library are similar to cytoskeleton mRNAs and may reflect a normal pathway of the cellular response after im infection with WSSV, and (b) primers flanking single or multiple SSRs with three or more repeats from shrimp ESTs could be an efficient approach to develop polymorphic markers useful for linkage mapping. Work is underway to map additional SSR-containing ESTs from this and other cDNA libraries as a plausible strategy to increase marker density in ShrimpMap.

改进的统计不相关最优鉴别矢量集

该文对统计不相关最优鉴别矢量集算法进行研究,在分析统计不相关最优鉴别矢量集算法的基础上提出了一种改进的方法。该方法在类内散布矩阵的特征空间中求解统计不相关最优鉴别矢量集。为了加快特征抽取速度,利用基于图像鉴别分析的维数压缩方法,对图像数据进行了压缩。在ORL和Yale人脸数据库的数值实验,验证本文所提出的方法的有效性。

大规模多数据库系统的互操作机制

Sharing data among disparate databases has so far mostly been achieved through some form of ad-hoc schema integration. This approach becomes less tractable as the number of participating database increases. In this paper,we first present the primary problems to be resolved in large multidatabase systems and discuss the autonomy and heteroheneity of large multidatabase systems and then describe a coalition agent mechanism to implement large multidatabase systems interoperation.

基于关系模型的含空值关系数据库的数据更新

本文以空值的完全语义为基础，以空值环境下基于５值（５ＶＬ）的选择运算为工具，深入研究了基于关于模型的含空值关系数据库的数据更新策略和实现算法

空值环境下关系数据库的更新 Ⅰ：扩展关系模型及基本运算

本文从空值语义及更新操作的关系出发，提出了一种新的扩展关系模型，用以组织更新操作下的含有空值的关系数据库中的信息．同时，定义了这种模型下的基本关系代数运算．为实现空值环境下关系数据库的数据更新奠定了基础。

空值环境下关系数据库的更新 Ⅱ：更新处理的插入、删除和修改操作算法

本文的这部分是以扩展模型为基础，以五种运算为工具，对空值环境下关系数据库的更新处理策略做了深入研究，并给出了相应的算法及算法分析。

冀东油田柳南地区新近系油藏剩余油形成及分布规律研究

This thesis is based on the research project of Study on the Geological Characteristics and Remaining Oil Distribution Law of Neogene Reservoirs in Liunan Area, which is one of the key research projects set by PetroChina Jidong Oilfield Company in 2006. The determination of remaining oil distribution and its saturation changes are the most important research contents for the development and production modification of oilfields in high water-cut phases. Liunan oilfield, located in Tangshan of Hebei Province geographically and in Gaoliu structural belt of Nanpu sag in Bohai Bay Basin structurally, is one of the earliest fields put into production of Jidong oilfield. Focusing on the development problems encountered during the production of the field, this thesis establishes the fine geological reservoir model through the study of reservoir properties such as fine beds correlation, sedimentary facies, micro structures, micro reservoir architecture, flow units and fluid properties. Using routine method of reservoir engineering and technology of reservoir numerical modeling, remaining oil distribution in the target beds of Liunan area is predicted successfully, while the controling factors of remaining oil distribution are illustrated, and the model of remaining oil distribution for fault-block structure reservoirs is established. Using staged-subdivision reservoir correlation and FZI study, the Strata in Liunan Area is subdivided step by step; oil sand body data-list is recompiled; diagram databases are established; plane and section configuration of monolayer sandstone body, and combination pattern of sandstone bodys are summarized. The study of multi-level staged subdivision for sedimentary micro-facies shows that the Lower member of Minghuazhen formation and the whole Guantao formation in Liunan Area belong to meandering river and braided river sedimentary facies respectively, including 8 micro facies such as after point bar, channel bar, channel, natural levee, crevasse splay, abandoned channel, flood plain and flood basin. Fine 3D geological modeling is performed through the application of advanced software and integration of geological, seismic logging and reservoir engineering data. High resolution numerical simulation is performed with a reserve fitting error less than 3%, an average pressure fitting fluctuation range lower than 2Mpa and an accumulate water cut fitting error less than 5%. In this way, the distribution law of the target reservoir in the study area is basically recognized. Eight major remaining oil distribution models are established after analysis of production status and production features in different blocks and different layers. In addition, fuzzy mathematics method is used to the integreted evaluation and prediction of abundant remaining oil accumulation area in major production beds and key sedimentary time units of the shallow strata in Liunan Area and corresponding modification comments are put forward. In summary, the establishment of fine reservoir geological model, reservoir numerical simulation and distribution prediction of remaining oil make a sound foundation for further stimulation of oilfield development performance.

Fast Contour Matching Using Approximate Earth Mover's Distance

Weighted graph matching is a good way to align a pair of shapes represented by a set of descriptive local features; the set of correspondences produced by the minimum cost of matching features from one shape to the features of the other often reveals how similar the two shapes are. However, due to the complexity of computing the exact minimum cost matching, previous algorithms could only run efficiently when using a limited number of features per shape, and could not scale to perform retrievals from large databases. We present a contour matching algorithm that quickly computes the minimum weight matching between sets of descriptive local features using a recently introduced low-distortion embedding of the Earth Mover's Distance (EMD) into a normed space. Given a novel embedded contour, the nearest neighbors in a database of embedded contours are retrieved in sublinear time via approximate nearest neighbors search. We demonstrate our shape matching method on databases of 10,000 images of human figures and 60,000 images of handwritten digits.

Logging and Recovery in a Highly Concurrent Database

This report addresses the problem of fault tolerance to system failures for database systems that are to run on highly concurrent computers. It assumes that, in general, an application may have a wide distribution in the lifetimes of its transactions. Logging remains the method of choice for ensuring fault tolerance. Generational garbage collection techniques manage the limited disk space reserved for log information; this technique does not require periodic checkpoints and is well suited for applications with a broad range of transaction lifetimes. An arbitrarily large collection of parallel log streams provide the necessary disk bandwidth.

C4.5: um recurso para geração de árvores de decisão.

O Sistema de Indução C4.5. Requerimentos-chave para a utilização do software. Um exemplo ilustrativo. Algumas dicas de uso.

Banco de dados de equipamentos: uma proposta para gerenciar bens patrimoniais de informática nas unidades da Embrapa.

Este trabalho descreve a proposta de um banco de dados de equipamentos de informática. Ele tem como objetivo informar ao usuário onde um determinado bem se encontra na unidade, assim como o responsável pelo equipamento, o número de patrimônio e demais dados pertinentes ao bem patrimonial. Em muitas situações, faz-se necessário localizar um determinado bem patrimonial, para fins de auditoria, substituição de equipamentos, manutenção, etc. Assim, informações precisas sobre um dado equipamento são necessárias para a administração de qualquer Unidade. O banco de dados de equipamentos permite inserir, remover, alterar e consultar dados pela Internet. O agente patrimonial é quem pode inserir, alterar e remover dados. Um usuário qualquer pode apenas consultar os dados. Assim, qualquer pessoa pode ver qualquer equipamento de informática sabendo-se apenas o número do patrimônio. Espera-se que este trabalho seja útil a todos os usuários que necessitarem gerenciar bens patrimoniais, localizar um equipamento, ou saber sobre sua disponibilidade.

Instalação e Configuração do PostgreSQL no Linux via código-fonte.

Apesar de exigir maior grau de dificuldade do que a instalação via pacotes, a instalação via código-fonte oferece uma infinidade de recursos em relação à primeira, tais como: definir a estrutura de diretórios para binários, bibliotecas, módulos, manuais e demais arquivos do SGBD conforme o desejado, o que facilita a organização, localização e manutenção do PostgreSQL; ativar suporte a um determinado idioma, para tradução de mensagens; construir suporte a determinadas linguagens ou módulos; definir alguns parâmetros padrões; além de conceber maior controle e segurança nas atualizações de versões do SGBD, evitando assim, atualizações automáticas indesejáveis por meio do sistema operacional e a conseqüente perda de bases de dados; entre outros. Para este trabalho, foi utilizado o sistema operacional Ubuntu Server 8.04.1, contudo, este tutorial é totalmente aplicável e compatível a outras versões Ubuntu, bem como a outras distribuições Linux, respeitando, é claro, as particularidades de algumas distribuições, como a estrutura de diretórios destes. Quanto ao SGBD PostgreSQL, foi adotado a versão 8.3.4, lançada em Setembro/2008, contudo, este tutorial se aplica também à versões inferiores 8.x.x deste SGBD.