Parametric model for the analysis of concrete expansion due to alkali-aggregate reaction

The alkali-aggregate reaction (AAR) is a chemical reaction that provokes a heterogeneous expansion of concrete and reduces important properties such as Young's modulus, leading to a reduction in the structure's useful life. In this study, a parametric model is employed to determine the spatial distribution of the concrete expansion, combining normalized factors that influence the reaction through an AAR expansion law. Optimization techniques were employed to adjust the numerical results and observations in a real structure. A three-dimensional version of the model has been implemented in a finite element commercial package (ANSYS(C)) and verified in the analysis of an accelerated mortar test. Comparisons were made between two AAR mathematical descriptions for the mechanical phenomenon, using the same methodology, and an expansion curve obtained from experiment. Some parametric studies are also presented. The numerical results compared very well with the experimental data validating the proposed method.

Trajectory Sensitivity Method and Master-Slave Synchronization to Estimate Parameters of Nonlinear Systems

A combination of trajectory sensitivity method and master-slave synchronization was proposed to parameter estimation of nonlinear systems. It was shown that master-slave coupling increases the robustness of the trajectory sensitivity algorithm with respect to the initial guess of parameters. Since synchronization is not a guarantee that the estimation process converges to the correct parameters, a conditional test that guarantees that the new combined methodology estimates the true values of parameters was proposed. This conditional test was successfully applied to Lorenz's and Chua's systems, and the proposed parameter estimation algorithm has shown to be very robust with respect to parameter initial guesses and measurement noise for these examples. Copyright (C) 2009 Elmer P. T. Cari et al.

Power Secant Method applied to natural frequency extraction of Timoshenko beam structures

This work deals with an improved plane frame formulation whose exact dynamic stiffness matrix (DSM) presents, uniquely, null determinant for the natural frequencies. In comparison with the classical DSM, the formulation herein presented has some major advantages: local mode shapes are preserved in the formulation so that, for any positive frequency, the DSM will never be ill-conditioned; in the absence of poles, it is possible to employ the secant method in order to have a more computationally efficient eigenvalue extraction procedure. Applying the procedure to the more general case of Timoshenko beams, we introduce a new technique, named ""power deflation"", that makes the secant method suitable for the transcendental nonlinear eigenvalue problems based on the improved DSM. In order to avoid overflow occurrences that can hinder the secant method iterations, limiting frequencies are formulated, with scaling also applied to the eigenvalue problem. Comparisons with results available in the literature demonstrate the strength of the proposed method. Computational efficiency is compared with solutions obtained both by FEM and by the Wittrick-Williams algorithm.

Applications of the Rietveld method to quantify the crystalline phases of Portland cement clinker doped with nickel and chromium

The effects of chromium or nickel oxide additions on the composition of Portland clinker were investigated by X-ray powder diffraction associated with pattern analysis by the Rietveld method. The co-processing of industrial waste in Portland cement plants is an alternative solution to the problem of final disposal of hazardous waste. Industrial waste containing chromium or nickel is hazardous and is difficult to dispose of. It was observed that in concentrations up to 1% in mass, the chromium or nickel oxide additions do not cause significant alterations in Portland clinker composition. (C) 2008 International Centre for Diffraction Data.

Method for early quantification of quiescent infections of Colletotrichum musae on bananas

Introduction. This protocol aims at detecting and quantifying quiescent infections of Colletotrichum musae on bananas. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. The materials required and details of the three steps of the protocol (fruit sampling, fruit ripening and anthracnose lesion quantification) are described. Possible troubleshooting is discussed. Results. The protocol results in the quantification of anthracnose lesions on the fruits, which makes it possible to predict postharvest losses due to anthracnose (peel rot), and also to propose a better management of postharvest fungicide applications.

A Simple and Fast Method for the Production and Characterization of Methylic and Ethylic Biodiesels from Tucum Oil via an Alkaline Route

A simple, fast, and complete route for the production of methylic and ethylic biodiesel from tucum oil is described. Aliquots of the oil obtained directly from pressed tucum (pulp and almonds) were treated with potassium methoxide or ethoxide at 40 degrees C for 40 min. The biodiesel form was removed from the reactor and washed with 0.1 M HCl aqueous solution. A simple distillation at 100 degrees C was carried out in order to remove water and alcohol species from the biodiesel. The oxidative stability index was obtained for the tucum oil as well as the methylic and ethylic biodiesel at 6.13, 2.90, and 2.80 h, for storage times higher than 8 days. Quality control of the original oil and of the methylic and ethylic biodiesels, such as the amount of glycerin produced during the transesterification process, was accomplished by the TLC, GC-MS, and FT-IR techniques. The results obtained in this study indicate a potential biofuel production by simple treatment of tucum, an important Amazonian fruit.

A Novel Hepatitis C Virus Genotyping Method Based on Liquid Microarray

The strategy used to treat HCV infection depends on the genotype involved. An accurate and reliable genotyping method is therefore of paramount importance. We describe here, for the first time, the use of a liquid microarray for HCV genotyping. This liquid microarray is based on the 5'UTR - the most highly conserved region of HCV - and the variable region NS5B sequence. The simultaneous genotyping of two regions can be used to confirm findings and should detect inter-genotypic recombination. Plasma samples from 78 patients infected with viruses with genotypes and subtypes determined in the Versant (TM) HCV Genotype Assay LiPA (version I; Siemens Medical Solutions, Diagnostics Division, Fernwald, Germany) were tested with our new liquid microarray method. This method successfully determined the genotypes of 74 of the 78 samples previously genotyped in the Versant (TM) HCV Genotype Assay LiPA (74/78, 95%). The concordance between the two methods was 100% for genotype determination (74/74). At the subtype level, all 3a and 2b samples gave identical results with both methods (17/17 and 7/7, respectively). Two 2c samples were correctly identified by microarray, but could only be determined to the genotype level with the Versant (TM) HCV assay. Genotype ""1'' subtypes (1a and 1b) were correctly identified by the Versant (TM) HCV assay and the microarray in 68% and 40% of cases, respectively. No genotype discordance was found for any sample. HCV was successfully genotyped with both methods, and this is of prime importance for treatment planning. Liquid microarray assays may therefore be added to the list of methods suitable for HCV genotyping. It provides comparable results and may readily be adapted for the detection of other viruses frequently co-infecting HCV patients. Liquid array technology is thus a reliable and promising platform for HCV genotyping.

A Method for Generation of Bone Marrow-Derived Macrophages from Cryopreserved Mouse Bone Marrow Cells

The broad use of transgenic and gene-targeted mice has established bone marrow-derived macrophages (BMDM) as important mammalian host cells for investigation of the macrophages biology. Over the last decade, extensive research has been done to determine how to freeze and store viable hematopoietic human cells; however, there is no information regarding generation of BMDM from frozen murine bone marrow (BM) cells. Here, we establish a highly efficient protocol to freeze murine BM cells and further generate BMDM. Cryopreserved murine BM cells maintain their potential for BMDM differentiation for more than 6 years. We compared BMDM obtained from fresh and frozen BM cells and found that both are similarly able to trigger the expression of CD80 and CD86 in response to LPS or infection with the intracellular bacteria Legionella pneumophila. Additionally, BMDM obtained from fresh or frozen BM cells equally restrict or support the intracellular multiplication of pathogens such as L. pneumophila and the protozoan parasite Leishmania (L.) amazonensis. Although further investigation are required to support the use of the method for generation of dendritic cells, preliminary experiments indicate that bone marrow-derived dendritic cells can also be generated from cryopreserved BM cells. Overall, the method described and validated herein represents a technical advance as it allows ready and easy generation of BMDM from a stock of frozen BM cells.

Automated supervised classification of variable stars in the CoRoT programme Method and application to the first four exoplanet fields

Aims. In this work, we describe the pipeline for the fast supervised classification of light curves observed by the CoRoT exoplanet CCDs. We present the classification results obtained for the first four measured fields, which represent a one-year in-orbit operation. Methods. The basis of the adopted supervised classification methodology has been described in detail in a previous paper, as is its application to the OGLE database. Here, we present the modifications of the algorithms and of the training set to optimize the performance when applied to the CoRoT data. Results. Classification results are presented for the observed fields IRa01, SRc01, LRc01, and LRa01 of the CoRoT mission. Statistics on the number of variables and the number of objects per class are given and typical light curves of high-probability candidates are shown. We also report on new stellar variability types discovered in the CoRoT data. The full classification results are publicly available.

Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence

Background: Mites (Acari) have traditionally been treated as monophyletic, albeit composed of two major lineages: Acariformes and Parasitiformes. Yet recent studies based on morphology, molecular data, or combinations thereof, have increasingly drawn their monophyly into question. Furthermore, the usually basal (molecular) position of one or both mite lineages among the chelicerates is in conflict to their morphology, and to the widely accepted view that mites are close relatives of Ricinulei. Results: The phylogenetic position of the acariform mites is examined through employing SSU, partial LSU sequences, and morphology from 91 chelicerate extant terminals (forty Acariformes). In a static homology framework, molecular sequences were aligned using their secondary structure as guide, whereby regions of ambiguous alignment were discarded, and pre-aligned sequences analyzed under parsimony and different mixed models in a Bayesian inference. Parsimony and Bayesian analyses led to trees largely congruent concerning infraordinal, well-supported branches, but with low support for inter-ordinal relationships. An exception is Solifugae + Acariformes (P. P = 100%, J. = 0.91). In a dynamic homology framework, two analyses were run: a standard POY analysis and an analysis constrained by secondary structure. Both analyses led to largely congruent trees; supporting a (Palpigradi (Solifugae Acariformes)) clade and Ricinulei as sister group of Tetrapulmonata with the topology (Ricinulei (Amblypygi (Uropygi Araneae))). Combined analysis with two different morphological data matrices were run in order to evaluate the impact of constraining the analysis on the recovered topology when employing secondary structure as a guide for homology establishment. The constrained combined analysis yielded two topologies similar to the exclusively molecular analysis for both morphological matrices, except for the recovery of Pedipalpi instead of the (Uropygi Araneae) clade. The standard (direct optimization) POY analysis, however, led to the recovery of trees differing in the absence of the otherwise well-supported group Solifugae + Acariformes. Conclusions: Previous studies combining ribosomal sequences and morphology often recovered topologies similar to purely morphological analyses of Chelicerata. The apparent stability of certain clades not recovered here, like Haplocnemata and Acari, is regarded as a byproduct of the way the molecular homology was previously established using the instrumentalist approach implemented in POY. Constraining the analysis by a priori homology assessment is defended here as a way of maintaining the severity of the test when adding new data to the analysis. Although the strength of the method advocated here is keeping phylogenetic information from regions usually discarded in an exclusively static homology framework; it still has the inconvenience of being uninformative on the effect of alignment ambiguity on resampling methods of clade support estimation. Finally, putative morphological apomorphies of Solifugae + Acariformes are the reduction of the proximal cheliceral podomere, medial abutting of the leg coxae, loss of sperm nuclear membrane, and presence of differentiated germinative and secretory regions in the testis delivering their products into a common lumen.

Heteroduplex formation and S1 digestion for mapping alternative splicing sites

The identification of alternatively spliced transcripts has contributed to a better comprehension of developmental mechanisms, tissue-specific physiological processes and human diseases. Polymerase chain reaction amplification of alternatively spliced variants commonly leads to the formation of heteroduplexes as a result of base pairing involving exons common between the two variants. S1 nuclease cleaves single-stranded loops of heteroduplexes and also nicks the opposite DNA strand. In order to establish a strategy for mapping alternative splice-prone sites in the whole transcriptome, we developed a method combining the formation of heteroduplexes between 2 distinct splicing variants and S1 nuclease digestion. For 20 consensuses identified here using this methodology, 5 revealed a conserved splice site after inspection of the cDNA alignment against the human genome (exact splice sites). For 8 other consensuses, conserved splice sites were mapped at 2 to 30 bp from the border, called proximal splice sites; for the other 7 consensuses, conserved splice sites were mapped at 40 to 800 bp, called distal splice sites. These latter cases showed a nonspecific activity of S1 nuclease in digesting double-strand DNA. From the 20 consensuses identified here, 5 were selected for reverse transcription-polymerase chain reaction validation, confirming the splice sites. These data showed the potential of the strategy in mapping splice sites. However, the lack of specificity of the S1 nuclease enzyme is a significant obstacle that impedes the use of this strategy in large-scale studies.

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

Background: Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve as therapeutic targets. Alternative splicing-enriched cDNA libraries have been used to explore the variability generated by alternative splicing. In this study, by combining the use of trapping heteroduplexes and RNA amplification, we developed a powerful approach that enables transcriptome-wide exploration of the AS repertoire for identifying AS variants associated with breast tumor cells modulated by ERBB2 (HER-2/neu) oncogene expression. Results: The human breast cell line (C5.2) and a pool of 5 ERBB2 over-expressing breast tumor samples were used independently for the construction of two AS-enriched libraries. In total, 2,048 partial cDNA sequences were obtained, revealing 214 alternative splicing sequence-enriched tags (ASSETs). A subset with 79 multiple exon ASSETs was compared to public databases and reported 138 different AS events. A high success rate of RT-PCR validation (94.5%) was obtained, and 2 novel AS events were identified. The influence of ERBB2-mediated expression on AS regulation was evaluated by capillary electrophoresis and probe-ligation approaches in two mammary cell lines (Hb4a and C5.2) expressing different levels of ERBB2. The relative expression balance between AS variants from 3 genes was differentially modulated by ERBB2 in this model system. Conclusions: In this study, we presented a method for exploring AS from any RNA source in a transcriptome-wide format, which can be directly easily adapted to next generation sequencers. We identified AS transcripts that were differently modulated by ERBB2-mediated expression and that can be tested as molecular markers for breast cancer. Such a methodology will be useful for completely deciphering the cancer cell transcriptome diversity resulting from AS and for finding more precise molecular markers.

Novel method for measuring nanofriction by atomic force microscope

The authors describe a novel approach to the measurement of nanofriction, and demonstrate the application of the method by measurement of the coefficient of friction for diamondlike carbon (DLC) on DLC, Si on DLC, and Si on Si surfaces. The technique employs an atomic force microscope in a mode in which the tip moves only in the z (vertical) direction and the sample surface is sloped. As the tip moves vertically on the sloped surface, lateral tip slipping occurs, allowing the cantilever vertical deflection and the frictional (lateral) force to be monitored as a function of tip vertical deflection. The advantage of the approach is that cantilever calibration to obtain its spring constants is not necessary. Using this method, the authors have measured friction coefficients, for load range 0 < L M 6 mu N, of 0.047 +/- 0.002 for Si on Si, 0.0173 +/- 0.0009 for Si on DLC, and 0.0080 +/- 0.0005 for DLC on DLC. For load range 9 < L < 13 mu N, the DLC on DLC coefficient of friction increased to 0.051 +/- 0.003. (C) 2008 American Vacuum Society.

Nuclear incoherent photoproduction of pi(0) and eta from 4 to 12 GeV

The mechanism of incoherent pi(0) and eta photoproduction from complex nuclei is investigated from 4 to 12 GeV with an extended version of the multicollisional Monte Carlo (MCMC) intranuclear cascade model. The calculations take into account the elementary photoproduction amplitudes via a Regge model and the nuclear effects of photon shadowing, Pauli blocking, and meson-nucleus final-state interactions. The results for pi(0) photoproduction reproduced for the first time the magnitude and energy dependence of the measured rations sigma(gamma A)/sigma(gamma N) for several nuclei (Be, C, Al, Cu, Ag, and Pb) from a Cornell experiment. The results for eta photoproduction fitted the inelastic background in Cornell's yields remarkably well, which is clearly not isotropic as previously considered in Cornell's analysis. With this constraint for the background, the eta -> gamma gamma. decay width was extracted using the Primakoff method, combining Be and Cu data [Gamma(eta ->gamma gamma) = 0.476(62) keV] and using Be data only [Gamma(eta ->gamma gamma) = 0.512(90) keV]; where the errors are only statistical. These results are in sharp contrast (similar to 50-60%) with the value reported by the Cornell group [Gamma(eta ->gamma gamma). = 0.324(46) keV] and in line with the Particle Data Group average of 0.510(26) keV.

Study of the influence of indium segregation on the optical properties of InGaAs/GaAs quantum wells via split-operator method

In the case of quantum wells, the indium segregation leads to complex potential profiles that are hardly considered in the majority of the theoretical models. The authors demonstrated that the split-operator method is useful tool for obtaining the electronic properties in these cases. Particularly, they studied the influence of the indium surface segregation in optical properties of InGaAs/GaAs quantum wells. Photoluminescence measurements were carried out for a set of InGaAs/GaAs quantum wells and compared to the results obtained theoretically via split-operator method, showing a good agreement.