A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

We report a method for studying global DNA methylation based on using bisulfite treatment of DNA and simultaneous PCR of multiple DNA repetitive elements, such as Alu elements and long interspersed nucleotide elements (LINE). The PCR product, which represents a pool of approximately 15000 genomic loci, could be used for direct sequencing, selective restriction digestion or pyrosequencing, in order to quantitate DNA methylation. By restriction digestion or pyrosequencing, the assay was reproducible with a standard deviation of only 2% between assays. Using this method we found that almost two-thirds of the CpG methylation sites in Alu elements are mutated, but of the remaining methylation target sites, 87% were methylated. Due to the heavy methylation of repetitive elements, this assay was especially useful in detecting decreases in DNA methylation, and this assay was validated by examining cell lines treated with the methylation inhibitor 5-aza-2'deoxycytidine (DAC), where we found a 1-16% decrease in Alu element and 18-60% LINE methylation within 3 days of treatment. This method can be used as a surrogate marker of genome-wide methylation changes. In addition, it is less labor intensive and requires less DNA than previous methods of assessing global DNA methylation.

A common Tabu search algorithm for the global optimization of engineering problems

A novel common Tabu algorithm for global optimizations of engineering problems is presented. The robustness and efficiency of the presented method are evaluated by using standard mathematical functions and hy solving a practical engineering problem. The numerical results show that the proposed method is (i) superior to the conventional Tabu search algorithm in robustness, and (ii) superior to the simulated annealing algorithm in efficiency. (C) 2001 Elsevier B.V. B.V. All rights reserved.

Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

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

Custodial symmetry and extensions of the standard model

We show that the extension of the approximate custodial SU(2)(L+R) global symmetry to all the Yukawa interactions of the standard model Lagrangian implies the introduction of sterile right-handed neutrinos and the seesaw mechanism in this sector. In this framework, the observed quark and lepton masses may be interpreted as an effect of physics beyond the standard model. The mechanism used for breaking this symmetry in the Yukawa sector could be different from the one at work in the vector boson sector. We give three model independent examples of these mechanisms.

Combined results of searches for the standard model Higgs boson in pp collisions at root s=7 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Search for the standard model Higgs boson decaying into two photons in pp collisions at root s=7 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Submucous myomas: A new presurgical classification to evaluate the viability of hysteroscopic surgical treatment - Preliminary report

STUDY OBJECTIVE: To develop a new preoperative classification of submucous myomas for evaluating the viability and the degree of difficulty of hysteroscopic myomectomy.DESIGN: Retrospective study (Canadian Task Force classification II-3)SETTING: University teaching hospitals.PATIENTS: Fifty-five patients who underwent hysteroscopic resection of submucous myomas.INTERVENTION: the possibility of total resection of the myoma, the operating time, the fluid deficit, and the frequency of any complications were considered. The myomas were classified according to the Classification of the European Society for Gynaecological Endoscopy (ESGE) and by our group's new classification (NC), which considers not only the degree of penetration of the myoma into the myometrium, but also adds in such parameters as the distance of the base of the myoma from the uterine wall, the size of the nodule (cm), and the topography of the uterine cavity. The Fisher's exact test, the Student's t test, and the analysis of variance test were used in the statistical analysis. A p value less than .05 in the two-tailed test was considered significant.MEASUREMENTS AND MAIN RESULTS: In 57 myomas, hysteroscopic surgery was considered complete. There was no significant difference among the three ESGE levels (0, 1, and 2). Using the NC, the difference between the numbers of complete surgeries was significant (p < .001) for the two levels (groups I and H). The difference between the operating times was significant for the two classifications. With respect to the fluid deficit, only the NC showed significant differences between the levels (p = .02).CONCLUSIONS: We believe that the NC gives more clues as to the difficulties of a hysteroscopic myomectomy than the standard ESGE classification. It should be stressed that the number of hysteroscopic myomectomies used in this analysis was low, and it would be interesting to evaluate the performance of the classification in a larger number of patients. (c) 2005 AAGL. All rights reserved.

New starches for the food industry: Curcuma longa and Curcuma zedoaria

The evolution of the food sector has increased interest in the identification of new starches with distinct properties. Curcuma longa and Curcuma zedoaria rhizomes, which are already used in industry to obtain food coloring and pharmaceutical products, may become commercially interesting as starch raw materials. This work aimed to characterize the starch of two Curcuma species. The results revealed that the rhizomes of two species showed low dry matter and high starch contents. The amylose contents of the starches (22% C. longa and 21% C. zedoaria) were similar to potato starch. The results of microscopic analysis showed flat triangular shape and the size was 20-30 mum for two starches. The final viscosity of C longa was high (740 RVU) and the pasting temperature was 81 degreesC. In C. zedoaria the final viscosity was 427 RVU and the pasting temperature was 78 degreesC. These results differed from standard commercially used natural starches. (C) 2003 Elsevier Ltd. All rights reserved.

Automatic classification of enzyme family in protein annotation

Most of the tasks in genome annotation can be at least partially automated. Since this annotation is time-consuming, facilitating some parts of the process - thus freeing the specialist to carry out more valuable tasks - has been the motivation of many tools and annotation environments. In particular, annotation of protein function can benefit from knowledge about enzymatic processes. The use of sequence homology alone is not a good approach to derive this knowledge when there are only a few homologues of the sequence to be annotated. The alternative is to use motifs. This paper uses a symbolic machine learning approach to derive rules for the classification of enzymes according to the Enzyme Commission (EC). Our results show that, for the top class, the average global classification error is 3.13%. Our technique also produces a set of rules relating structural to functional information, which is important to understand the protein tridimensional structure and determine its biological function. © 2009 Springer Berlin Heidelberg.

Classification of petroleum well drilling operations with a hybrid particle swarm/ant colony algorithm

This paper describes an investigation of the hybrid PSO/ACO algorithm to classify automatically the well drilling operation stages. The method feasibility is demonstrated by its application to real mud-logging dataset. The results are compared with bio-inspired methods, and rule induction and decision tree algorithms for data mining. © 2009 Springer Berlin Heidelberg.

The rise in global demand for ethanol and poverty in Brazil

Incluye Bibliografía

The rise in global demand for ethanol and poverty in Brazil

Includes bibliography

The transformation of the North American apparel industry: is NAFTA a curse or a blessing?

Includes bibliography

The Mexican maquila industry and the environment: an overview of the issues

Includes bibliography

A case study of concurrent engineering application on the development of parts for the white goods industry in Brazil

This classical way to manage product development processes for massive production seems to be changing: high pressure for cost reduction, higher quality standards, markets reaching for innovation lead to the necessity of new tools for development control. Into this, and learning from the automotive and aerospace industries factories from other segments are starting to understand and apply manufacturing and assembly oriented projects to ease the task of generate goods and from this obtain at least a part of the expected results. This paper is intended to demonstrate the applicability of the concepts of Concurrent Engineering and DFM/DFA (Design for Manufacturing and Assembly) in the development of products and parts for the White Goods industry in Brazil (major appliances as refrigerators, cookers and washing machines), showing one case concerning the development and releasing of a component. Finally is demonstrated in a short term how was reached a solution that could provide cost savings and reduction on the time to delivery using those techniques.