The fish zonation of the Itanha,m river basin in the Atlantic Forest of southeast Brazil

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

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.

Um novo método para quantificar mercúrio orgânico (Hg orgânico) empregando a espectrometria de fluorescência atômica do vapor frio

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

O problema de corte de estoque em indústrias de móveis de pequeno e médio portes

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

Abordagens complementares para problemas de p-medianas

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

Métodos de geração de colunas para problemas de atribuição

Este trabalho apresenta métodos de geração de colunas para dois importantes problemas de atribuição: o Problema Generalizado de Atribuição (PGA) e o Problema de Atribuição de Antenas a Comutadores (PAAC). O PGA é um dos mais representativos problemas de Otimização Combinatória e consiste em otimizar a atribuição de n tarefas a m agentes, de forma que cada tarefa seja atribuída a exatamente um agente e a capacidade de cada agente seja respeitada. O PAAC consiste em atribuir n antenas a m comutadores em uma rede de telefonia celular, de forma a minimizar os custos de cabeamento entre antenas e comutadores e os custos de transferência de chamadas entre comutadores. A abordagem tradicional de geração de colunas é comparada com as propostas neste trabalho, que utilizam a relaxação lagrangeana/surrogate. São apresentados testes computacionais que demonstram a efetividade dos algoritmos propostos.

Um modelo de otimização inteira mista e heurísticas relax and fix para a programação da produção de fábricas de refrigerantes de pequeno porte

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

Um problema de programação da produção numa fundição automatizada

Este trabalho apresenta a modelagem de um problema particular de Programação da Produção numa Fundição Automatizada e sua resolução por um algoritmo de busca heurística, que explora a estrutura do problema.

Economic design of two-stage (X)over-bar charts: the Markov chain approach

When the (X) over bar chart is in use, samples are regularly taken from the process, and their means are plotted on the chart. In some cases, it is too expensive to obtain the X values, but not the values of a correlated variable Y. This paper presents a model for the economic design of a two-stage control chart, that is. a control chart based on both performance (X) and surrogate (Y) variables. The process is monitored by the surrogate variable until it signals an out-of-control behavior, and then a switch is made to the (X) over bar chart. The (X) over bar chart is built with central, warning. and action regions. If an X sample mean falls in the central region, the process surveillance returns to the (Y) over bar chart. Otherwise. The process remains under the (X) over bar chart's surveillance until an (X) over bar sample mean falls outside the control limits. The search for an assignable cause is undertaken when the performance variable signals an out-of-control behavior. In this way, the two variables, are used in an alternating fashion. The assumption of an exponential distribution to describe the length of time the process remains in control allows the application of the Markov chain approach for developing the cost function. A study is performed to examine the economic advantages of using performance and surrogate variables. (C) 2003 Elsevier B.V. All rights reserved.

A column generation approach to capacitated p-median problems

The Capacitated p-median problem (CPMP) seeks to solve the optimal location of p facilities, considering distances and capacities for the service to be given by each median. In this paper we present a column generation approach to CPMP. The identified restricted master problem optimizes the covering of 1-median clusters satisfying the capacity constraints, and new columns are generated considering knapsack subproblems. The Lagrangean/surrogate relaxation has been used recently to accelerate subgradient like methods. In this work the Lagrangean/surrogate relaxation is directly identified from the master problem dual and provides new bounds and new productive columns through a modified knapsack subproblem. The overall column generation process is accelerated, even when multiple pricing is observed. Computational tests are presented using instances taken from real data from Sao Jose dos Campos' city.

Modeling hourly diffuse solar-radiation in the city of São Paulo using a neural-network technique

dIn this work, a perceptron neural-network technique is applied to estimate hourly values of the diffuse solar-radiation at the surface in São Paulo City, Brazil, using as input the global solar-radiation and other meteorological parameters measured from 1998 to 2001. The neural-network verification was performed using the hourly measurements of diffuse solar-radiation obtained during the year 2002. The neural network was developed based on both feature determination and pattern selection techniques. It was found that the inclusion of the atmospheric long-wave radiation as input improves the neural-network performance. on the other hand traditional meteorological parameters, like air temperature and atmospheric pressure, are not as important as long-wave radiation which acts as a surrogate for cloud-cover information on the regional scale. An objective evaluation has shown that the diffuse solar-radiation is better reproduced by neural network synthetic series than by a correlation model. (C) 2004 Elsevier Ltd. All rights reserved.

Reappraisal of immunohistochemical profiling of special histological types of breast carcinomas: a study of 121 cases of eight different subtypes

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

Complete replacement of the mitochondrial genotype in a Bos indicus calf reconstructed by nuclear transfer to a bos taurus oocyte

Due to the exclusively maternal inheritance of mitochondria, mitochondrial genotypes can be coupled to a particular nuclear genotype by continuous mating of founder females and their female offspring to males of the desired nuclear genotype. However, backcrossing is a gradual procedure that, apart from being lengthy, cannot ascertain that genetic and epigenetic changes will modify the original nuclear genotype. Animal cloning by nuclear transfer using host ooplasm carrying polymorphic mitochondrial genomes allows, among other biotechnology applications, the coupling of nuclear and mitochondrial genotypes of diverse origin within a single generation. Previous attempts to use Bos taurus oocytes as hosts to transfer nuclei from unrelated species led to the development to the blastocyst stage but none supported gestation to term. Our aim in this study was to determine whether B. taurus oocytes support development of nuclei from the closely related B. indicus cattle and to examine the fate of their mitochondrial genotypes throughout development. We show that indicus:taurus reconstructed oocytes develop to the blastocyst stage and produce live offspring after transfer to surrogate cows. We also demonstrate that, in reconstructed embryos, donor cell-derived mitochondria undergo a stringent genetic drift during early development leading, in most cases, to a reduction or complete elimination of B. indicus mtDNA. These results demonstrate that cross-subspecies animal cloning is a viable approach both for matching diverse nuclear and cytoplasmic genes to create novel breeds of cattle and for rescuing closely related endangered cattle.

Immune reconstitution in HIV-1 infected patients treated for two years with highly active antiretroviral therapy

The aim of this paper was to evaluate the immune reconstitution of HIV-1 patients subjected to highly active antiretroviral therapy (HAART) for two years or more according to CD 45RA and CD 45RO cell count; determination of IL-2, IFN-γ, IL-4, IL-10 and TNF-α serum levels; CD 4 + T and CD 8 + T lymphocyte count; and plasma viral load (VL) determination. For this purpose, a cross sectional study was carried out in the Tropical Diseases Area, Botucatu School of Medicine, São Paulo State University, UNESP, Botucatu, São Paulo, Brazil. Between June 2001 and April 2002, 37 HIV-1 infected patients were evaluated, 13 with treatment indication but untreated (G1), 9 subjected to HAART for 5-7 months (G2), and 15 treated for two years or more (G3); both treated groups used medication regularly and without failure. Forty-nine normal individuals were studied as controls (GC-1 and GC-2). There was a tendency (p<0.10) for the predominance of two nucleoside reverse transcriptase inhibitors (NRTI) associated with one non-nucleoside reverse transcriptase inhibitor (NNRTI) regimen in G2; and two NRTI associated with a protease inhibitor (PI) in G3. Statistical differences between groups were seen for CD 45RA (G1<[G3=GC-2]; p<0.05) and CD 45RO (G1[G2=G3]; p<0.001), TNF-α serum determination ([G1>G3; G2=intermediate]>GC-1; p<0.001), IL-2 (G1<[G2=G3=GC-1]; p<0.01), IFN-γ ([G1=GC-1]>[GC-2=G3]; p<0.001), IL-4 and IL-10 ([G1=G2=G3]>GC-1; p<0.001), serum cytokine profiles, with a higher proportion of subtype 2 in G1 and mature subtype 0 in G2 and G3 (p<0.005). There was no statistical difference for CD 8 + T lymphocyte counts (G1=G2=G3; p<0.50). Consistency was seen between positive correlations of profile 1 definer cytokines (IL-2 and IFN-γ), CD 45RA and CD 45RO cells, and CD 4 + T lymphocyte counts and between positive correlations of profile 2 definer cytokines (IL-4 and IL-10) with TNF-α, and VL. The negative correlations were also consistent as they expressed the inverse of the positives. The variables with the highest number of correlations were IL-2, IFN-γ, and VL, followed by CD 45RA and CD 45RO cells, and IL-10. The variables with the lowest number of correlations were CD 4 + T and CD 8 + T lymphocytes. The results express the partial but important immune reconstitution in HIV-1 infected individuals with the interference of HAART and the importance of cytokines especially IL-2 and IFN-γ, and CD 45RA and CD 45RO cells as surrogate markers of this reconstitution.

Poincaré plot indexes of heart rate variability: Relationships with other nonlinear variables

The Poincaré plot for heart rate variability analysis is a technique considered geometrical and non-linear, that can be used to assess the dynamics of heart rate variability by a representation of the values of each pair of R-R intervals into a simplified phase space that describes the system's evolution. The aim of the present study was to verify if there is some correlation between SD1, SD2 and SD1/SD2 ratio and heart rate variability nonlinear indexes either in disease or healthy conditions. 114 patients with arterial coronary disease and 65 healthy subjects underwent 30. minute heart rate registration, in supine position and the analyzed indexes were as follows: SD1, SD2, SD1/SD2, Sample Entropy, Lyapunov Exponent, Hurst Exponent, Correlation Dimension, Detrended Fluctuation Analysis, SDNN, RMSSD, LF, HF and LF/HF ratio. Correlation coefficients between SD1, SD2 and SD1/SD2 indexes and the other variables were tested by the Spearman rank correlation test and a regression analysis. We verified high correlation between SD1/SD2 index and HE and DFA (α1) in both groups, suggesting that this ratio can be used as a surrogate variable. © 2013 Elsevier B.V.