Microsatellite loci isolation from river buffalo using enriched partial genomic libraries

The extensive use of buffalo in agriculture, especially in developing countries, begs for genetic resources to evaluate and improve traits important to local and regional economies. Brazil presents the largest water buffalo populations in the New World, with 1 1 million heads including swamp and river types. To design rational breeding strategies for optimum utilization and conservation of available genetic variability in the Brazilian buffalo's population, it is essential to understand their genetic architecture and relationship among various breeds. This depends, in part, on the knowledge of their genetic structure based on molecular markers like microsatellites. In the present study, we developed six enriched partial genomic libraries for river buffalo using selective hybridization methods. Genomic DNA was hybridized with six different arrays of repeat motif, 5' biotinylated - (CA)(15), (CT)(15), (AGG)(8), (GAAA)(8), (GATA)(8), (AAAAC)(8) - and bound to streptavidin coated beads. The cloning process generated a total of 1920 recombinant clones. Up to date, 487 were directly sequenced for the presence of repeats, from which 13 have been positive for presence of repeats as follows: 9 for di-nucleotide repeats, 3 for tri-nucleotide repeats and 1 for tetra-nucleotide repeat. PCR primer pairs for the isolated microsatellites are under construction to determine optimum annealing temperature. These microsatellites will be useful for studies involving phylogenetic relationships, genome mapping and genetic diversity analysis within buffalo populations worldwide.

Branch formation in Pulvinularia suecica (Nostocales, Cyanoprokaryota) and considerations on the classification of dichotomously and pseudodichotomously branched genera

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The hierarchical model of branch planning with random coefficients

We consider the management branch model where the random resources of the subsystem are given by the exponential distributions. The determinate equivalent is a block structure problem of quadratic programming. It is solved effectively by means of the decomposition method, which is based on iterative aggregation. The aggregation problem of the upper level is resolved analytically. This overcomes all difficulties concerning the large dimension of the main problem.

Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Continuation load flow using automatically determined branch megawatt losses as parameters

The conventional Newton's method is considered to be inadequate for the computation of the maximum loading point (MLP) of power systems since: (i) it encounters difficulties in the vicinity of the MLP: and (ii) the load flow Jacobian matrix becomes singular at the MLP. It is well known that continuation methods are powerful and useful tools that are able to trace the solution PV curve without experiencing such diffculties. However, continuation methods require a parameterisation so that a modified, well conditioned set of load flow equations is obtained. In particular, the Jacobian matrix associated with this modified set of equations should not be singular at the MLP. The authors propose that the actual power losses in transmission branches (lines and transformers) are used to parameterise the approach. Specific procedures for the automatic determination of the most appropriate parameter (branch) are proposed. Such procedures include the utilisation of fast voltage-stability indices. Simulation results are presented to show that the proposed method is able to trace the whole solution PV curve very efficiently.

TRICUT: a program to clip triangle meshes using the rapid and triangle libraries and the visualization toolkit

An efficient technique to cut polygonal meshes as a step in the geometric modeling of topographic and geological data has been developed. In boundary represented models of outcropping strata and faulted horizons polygonal meshes often intersect each other. TRICUT determines the line of intersection and re-triangulates the area of contact. Along this line the mesh is split in two or more parts which can be selected for removal. The user interaction takes place in the 3D-model space. The intersection, selection and removal are under graphic control. The visualization of outcropping geological structures in digital terrain models is improved by determining intersections against a slightly shifted terrain model. Thus, the outcrop line becomes a surface which overlaps the terrain in its initial position. The area of this overlapping surface changes with respect to the strike and dip of the structure, the morphology and the offset. Some applications of TRICUT on different real datasets are shown. TRICUT is implemented in C+ + using the Visualization Toolkit in conjunction with the RAPID and TRIANGLE libraries. The program runs under LINUX and UNIX using the MESA OpenGL library. This work gives an example of solving a complex 3D geometric problem by integrating available robust public domain software. (C) 2002 Elsevier B.V. Ltd. All rights reserved.

Constructive heuristic algorithm in branch-and-bound structure applied to transmission network expansion planning

A constructive heuristic algorithm to solve the transmission system expansion planning problem is proposed with the aim of circumventing some critical problems of classical heuristic algorithms that employ relaxed mathematical models to calculate a sensitivity index that guides the circuit additions. The proposed heuristic algorithm is in a branch-and-bound algorithm structure, which can be used with any planning model, such as Transportation model, DC model, AC model or Hybrid models. Tests of the proposed algorithm are presented on real Brazilian systems.

Branch and bound algorithm for transmission system expansion planning using a transportation model

A method for optimal transmission network expansion planning is presented. The transmission network is modelled as a transportation network. The problem is solved using hierarchical Benders decomposition in which the problem is decomposed into master and slave subproblems. The master subproblem models the investment decisions and is solved using a branch-and-bound algorithm. The slave subproblem models the network operation and is solved using a specialised linear program. Several alternative implementations of the branch-and-bound algorithm have been rested. Special characteristics of the transmission expansion problem have been taken into consideration in these implementations. The methods have been tested on various test systems available in the literature.

Specialised branch-and-bound algorithm for transmission network expansion planning

An algorithm is presented that finds the optimal plan long-term transmission for till cases studied, including relatively large and complex networks. The knowledge of optimal plans is becoming more important in the emerging competitive environment, to which the correct economic signals have to be sent to all participants. The paper presents a new specialised branch-and-bound algorithm for transmission network expansion planning. Optimality is obtained at a cost, however: that is the use of a transportation model for representing the transmission network, in this model only the Kirchhoff current law is taken into account (the second law being relaxed). The expansion problem then becomes an integer linear program (ILP) which is solved by the proposed branch-and-bound method without any further approximations. To control combinatorial explosion the branch- and bound algorithm is specialised using specific knowledge about the problem for both the selection of candidate problems and the selection of the next variable to be used for branching. Special constraints are also used to reduce the gap between the optimal integer solution (ILP program) and the solution obtained by relaxing the integrality constraints (LP program). Tests have been performed with small, medium and large networks available in the literature.

Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98 % minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65(.)2 %) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10(.)9 %), Spirochaetes (4(.)3 %), Bacteroidetes (6(.)5 %), Actinobacteria (2(.)2 %) and Deferribacteres (2(.)2 %). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.

Transmission system expansion planning by a branch-and-bound algorithm

A branch and bound (B& B) algorithm using the DC model, to solve the power system transmission expansion planning by incorporating the electrical losses in network modelling problem is presented. This is a mixed integer nonlinear programming (MINLP) problem, and in this approach, the so-called fathoming tests in the B&B algorithm were redefined and a nonlinear programming (NLP) problem is solved in each node of the B& B tree, using an interior-point method. Pseudocosts were used to manage the development of the B&B tree and to decrease its size and the processing time. There is no guarantee of convergence towards global optimisation for the MINLP problem. However, preliminary tests show that the algorithm easily converges towards the best-known solutions or to the optimal solutions for all the tested systems neglecting the electrical losses. When the electrical losses are taken into account, the solution obtained using the Garver system is better than the best one known in the literature.

Planejamento de Fontes Reativas em Sistemas de Energia Elétrica utilizando a técnica de Decomposição de Benders e o algoritmo de Branch-and-Bound

This paper presents the Benders decomposition technique and Branch and Bound algorithm used in the reactive power planning in electric energy systems. The Benders decomposition separates the planning problem into two subproblems: an investment subproblem (master) and the operation subproblem (slave), which are solved alternately. The operation subproblem is solved using a successive linear programming (SLP) algorithm while the investment subproblem, which is an integer linear programming (ILP) problem with discrete variables, is resolved using a Branch and Bound algorithm especially developed to resolve this type of problem.

A branch-and-bound algorithm for the multi-stage transmission expansion planning

This work presents a branch-and-bound algorithm to solve the multi-stage transmission expansion planning problem. The well known transportation model is employed, nevertheless the algorithm can be extended to hybrid models or to more complex ones such as the DC model. Tests with a realistic power system were carried out in order to show the performance of the algorithm for the expansion plan executed for different time frames. © 2005 IEEE.