A boundary element formulation for analysis of elastoplastic plates with geometrical nonlinearity

In this paper a new boundary element method formulation for elastoplastic analysis of plates with geometrical nonlinearities is presented. The von Mises criterion with linear isotropic hardening is considered to evaluate the plastic zone. Large deflections are assumed but within the context of small strain. To derive the boundary integral equations the von Karman`s hypothesis is taken into account. An initial stress field is applied to correct the true stresses according to the adopted criterion. Isoparametric linear elements are used to approximate the boundary unknown values while triangular internal cells with linear shape function are adopted to evaluate the domain value influences. The nonlinear system of equations is solved by using an implicit scheme together with the consistent tangent operator derived along the paper. Numerical examples are presented to demonstrate the accuracy and the validity of the proposed formulation.

GENERALIZED FINITE ELEMENT METHOD FOR NONLINEAR THREE-DIMENSIONAL ANALYSIS OF SOLIDS

The Generalized Finite Element Method (GFEM) is employed in this paper for the numerical analysis of three-dimensional solids tinder nonlinear behavior. A brief summary of the GFEM as well as a description of the formulation of the hexahedral element based oil the proposed enrichment strategy are initially presented. Next, in order to introduce the nonlinear analysis of solids, two constitutive models are briefly reviewed: Lemaitre`s model, in which damage and plasticity are coupled, and Mazars`s damage model suitable for concrete tinder increased loading. Both models are employed in the framework of a nonlocal approach to ensure solution objectivity. In the numerical analyses carried out, a selective enrichment of approximation at regions of concern in the domain (mainly those with high strain and damage gradients) is exploited. Such a possibility makes the three-dimensional analysis less expensive and practicable since re-meshing resources, characteristic of h-adaptivity, can be minimized. Moreover, a combination of three-dimensional analysis and the selective enrichment presents a valuable good tool for a better description of both damage and plastic strain scatterings.

A hybrid-mixed finite element formulation for the geometrically exact analysis of three-dimensional framed structures

This paper addresses the development of a hybrid-mixed finite element formulation for the quasi-static geometrically exact analysis of three-dimensional framed structures with linear elastic behavior. The formulation is based on a modified principle of stationary total complementary energy, involving, as independent variables, the generalized vectors of stress-resultants and displacements and, in addition, a set of Lagrange multipliers defined on the element boundaries. The finite element discretization scheme adopted within the framework of the proposed formulation leads to numerical solutions that strongly satisfy the equilibrium differential equations in the elements, as well as the equilibrium boundary conditions. This formulation consists, therefore, in a true equilibrium formulation for large displacements and rotations in space. Furthermore, this formulation is objective, as it ensures invariance of the strain measures under superposed rigid body rotations, and is not affected by the so-called shear-locking phenomenon. Also, the proposed formulation produces numerical solutions which are independent of the path of deformation. To validate and assess the accuracy of the proposed formulation, some benchmark problems are analyzed and their solutions compared with those obtained using the standard two-node displacement/ rotation-based formulation.

Finite element and dimensional analysis algorithm for the prediction of mechanical properties of bulk materials and thin films

In this work, the applicability of a new algorithm for the estimation of mechanical properties from instrumented indentation data was studied for thin films. The applicability was analyzed with the aid of both three-dimensional finite element simulations and experimental indentation tests. The numerical approach allowed studying the effect of the substrate on the estimation of mechanical properties of the film, which was conducted based on the ratio h(max)/l between maximum indentation depth and film thickness. For the experimental analysis, indentation tests were conducted on AISI H13 tool steel specimens, plasma nitrated and coated with TiN thin films. Results have indicated that, for the conditions analyzed in this work, the elastic deformation of the substrate limited the extraction of mechanical properties of the film/substrate system. This limitation occurred even at low h(max)/l ratios and especially for the estimation of the values of yield strength and strain hardening exponent. At indentation depths lower than 4% of the film thickness, the proposed algorithm estimated the mechanical properties of the film with accuracy. Particularly for hardness, precise values were estimated at h(max)/l lower than 0.1, i.e. 10% of film thickness. (C) 2010 Published by Elsevier B.V.

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (similar to 2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.

Endophytic Colonization of Potato (Solanum tuberosum L.) by a Novel Competent Bacterial Endophyte, Pseudomonas putida Strain P9, and Its Effect on Associated Bacterial Communities

Pseudomonas putida strain P9 is a novel competent endophyte from potato. P9 causes cultivar-dependent suppression of Phytophthora infestans. Colonization of the rhizoplane and endosphere of potato plants by P9 and its rifampin-resistant derivative P9R was studied. The purposes of this work were to follow the fate of P9 inside growing potato plants and to establish its effect on associated microbial communities. The effects of P9 and P9R inoculation were studied in two separate experiments. The roots of transplants of three different cultivars of potato were dipped in suspensions of P9 or P9R cells, and the plants were planted in soil. The fate of both strains was followed by examining colony growth and by performing PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Colonies of both strains were recovered from rhizoplane and endosphere samples of all three cultivars at two growth stages. A conspicuous band, representing P9 and P9R, was found in all Pseudomonas PCR-DGGE fingerprints for treated plants. The numbers of P9R CFU and the P9R-specific band intensities for the different replicate samples were positively correlated, as determined by linear regression analysis. The effects of plant growth stage, genotype, and the presence of P9R on associated microbial communities were examined by multivariate and unweighted-pair group method with arithmetic mean cluster analyses of PCR-DGGE fingerprints. The presence of strain P9R had an effect on bacterial groups identified as Pseudomonas azotoformans, Pseudomonas veronii, and Pseudomonas syringae. In conclusion, strain P9 is an avid colonizer of potato plants, competing with microbial populations indigenous to the potato phytosphere. Bacterization with a biocontrol agent has an important and previously unexplored effect on plant-associated communities.

Carotenoids production from a newly isolated Sporidiobolus pararoseus strain by submerged fermentation

This work aimed at evaluating the total carotenoids production by a newly isolated Sporidiobolus pararoseus. Bioproduction was carried out in an orbital shaker, using 10% (w/v) of inoculum (25 A degrees C, 180 rpm for 35 h), incubated for 120 h in a dark room. Liquid N(2) and dimethylsulphoxide (DMSO) were used for cell rupture, and carotenoids were extracted with a solution of acetone/methanol (7:3, v/v). Optimization of carotenoids bioproduction was achieved by experimental design technique. Initially, a Plackett-Burman design was used for the screening of the most important factors, after the statistical analysis, a complete second-order design was carried out to optimize the concentration of total carotenoids in a conventional medium. Maximum concentration of 856 mu g/L of total carotenoids was obtained in a medium containing 60 g/L of glucose, 15 g/L of peptone, and 15 g/L of malt extract, 25 A degrees C, initial pH 4.0 and 180 rpm. Fermentation kinetics showed that the maximum concentration of total carotenoids was reached after 102 h of fermentation and that carotenoids bioproduction was associated with cell growth.

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase from Y strain

Trypanosoma cruzi is the etiological agent of Chagas` disease, a pathogenesis that affects millions of people in Latin America. Here, we report the crystal structure of dihydroorotate dehydrogenase (DHODH) from T cruzi strain Y solved at 2.2 angstrom resolution. DHODH is a flavin mononucleotide containing enzyme, which catalyses the oxidation Of L-dihydroorotate to orotate, the fourth step and only redox reaction in the de novo biosynthesis of pyrimidine nucleotides. Genetic studies have shown that DHODH is essential for T cruzi survival, validating the idea that this enzyme can be considered an attractive target for the development of antichagasic drugs. In our work, a detailed analysis of T cruzi DHODH crystal structure has allowed us to suggest potential sites to be further exploited for the design of highly specific inhibitors through the technology of structure-based drug design. (c) 2008 Elsevier Inc. All rights reserved.

Phenotypic analysis of genes whose mRNA accumulation is dependent on calcineurin in Aspergillus fumigatus

Calcineurin plays an important role in the control of cell morphology and virulence in fungi. Calcineurin is a serine/threonine-specific protein phosphatase heterodimer consisting of a catalytic subunit A and a regulatory subunit B. A mutant of Aspergillus fumigatus lacking the calcineurin A (calA) catalytic subunit exhibited defective hyphal morphology related to apical extension and branching growth, which resulted in drastically decreased filamentation. Here, we investigated which pathways are influenced by A. fumigatus calcineurin during proliferation by comparatively determining the transcriptional profile of A. fumigatus wild type and Delta calA mutant strains. Our results showed that the mitochondrial copy number is reduced in the Delta calA mutant strain, and the mutant has increased alternative oxidase (aoxA) mRNA accumulation and activity. Furthermore, we identified four genes that encode transcription factors that have increased mRNA expression in the Delta calA mutant. Deletion mutants for these transcription factors had reduced susceptibility to itraconazole, caspofungin, and sodium dodecyl sulfate (SDS). (C) 2009 Elsevier Inc. All rights reserved.

Differences Between ""Classical"" Risk Factors for Infections Caused by Methicillin-Resistant Staphylococcus aureus (MRSA) and Risk Factors for Nosocomial Bloodstream Infections Caused by Multiple Clones of the Staphylococcal Cassette Chromosome mec Type IV MRSA Strain

OBJECTIVE. To identify risk factors associated with nosocomial bloodstream infections caused by multiple clones of the staphylococcal cassette chromosome mec (SCCmec) type IV strain of methicillin-resistant Staphylococcus aureus (MRSA). DESIGN. An unmatched case-control study (at a ratio of 1 : 2) performed during the period from October 2002 through September 2003. SETTING. A 2,000-bed tertiary care teaching hospital affiliated with the University of Sao Paulo in Sao Paulo, Brazil. METHODS. Case patients (n = 30) were defined either as patients who had a bloodstream infection due to SCCmec type IV strains of MRSA diagnosed at least 48 hours after hospital admission or as neonates with the infection who were born in the hospital. Control patients (n = 60) were defined as patients with SCCmec type III MRSA infection diagnosed at least 48 hours after hospital admission. Genes n = 60 encoding virulence factors were studied in the isolates recovered from case patients, and molecular typing of the SCCmec type IV MRSA isolates was also done by pulsed-field gel electrophoresis and multilocus sequence typing. RESULTS. In multivariate analysis, the following 3 variables were significantly associated with having a nosocomial bloodstream infection caused by SCCmec type IV strains of MRSA: an age of less than 1 year, less frequent use of a central venous catheter (odds ratio [OR], 0.07 [95% confidence interval {CI}, 0.02-0.28]; P = .001), and female sex. A second analysis was performed that excluded the case and Pp. 001 control patients from the neonatal unit, and, in multivariate analysis, the following variables were significantly associated with having a nosocomial bloodstream infection caused by SCCmec type IV strains of MRSA: less frequent use of a central venous catheter (OR, 0.12 [95% CI, 0.03-0.55]; P = .007), lower Acute Physiology and Chronic Health Evaluation II score on admission (OR, 0.14 [95% CI, 0.03-0.61];), less frequent surgery (OR, 0.21 [95% CI, 0.06-0.83];), and female sex (OR, 5.70 [95% CI, 1.32-24.66]; P =.020). P = .009 Pp. 025 Pp). Of the 29 SCCmec type IV MRSA isolates recovered from case patients, none contained the Panton-Valentine leukocidin, gamma-hemolysin, enterotoxin B or C, or toxic shock syndrome toxin-1. All of the isolates contained genes for the LukE-LukD leukocidin and alpha-hemolysin. Genes for enterotoxin A were present in 1 isolate, and genes for beta-hemolysin were present in 3 isolates. CONCLUSIONS. ""Classical"" risk factors do not apply to patients infected with the SCCmec type IV strain of MRSA, which is an important cause of nosocomial bacteremia. This strain infects a patient population that is less ill and has had less frequent invasive procedures than a patient population infected with the multidrug-resistant strain of SCCmec type III MRSA. We found that virulence factors were rare and that Panton-Valentine leukocidin was absent. There were multiple clones of the SCCmec type IV strain in our hospital. Children under 1 year of age were at a higher risk. There was a predominant clone ( sequence type 5) in this patient population.

Complete genome analysis of a rabies virus isolate from Brazilian wild fox

The complete genome sequence of wild-type rabies virus (RABV) isolated from a wild Brazilian hoary fox (Dusicyon sp.), the BR-Pfx1 isolate, was determined and compared with fixed RABV strains. The genome structure and organization of the BR-Pfx1 isolate were composed of 11,924 nt and included the five standard genes of rhabdoviruses. Sequences of mRNA start and stop signals for transcription were highly conserved among all structural protein genes of the BR-Pfx1 isolate. All amino acid residues in the glycoprotein (G) gene associated with pathogenicity were retained in the BR-Pfx1 isolate, while unique amino acid substitutions were found in antigenic region I of the nucleoprotein gene and III of G. These results suggest that although the standard genome structure and organization of the RABV isolate are common between the BR-Pfx1 isolate and fixed RABV strains, the unique amino acid substitutions in functional sites of the BR-Pfx1 isolate may result in different biological characteristics from fixed RABV strains.

Characterization by restriction fragment length polymorphism and sequence analysis of field and vaccine strains of infectious laryngotracheitis virus involved in severe outbreaks

At the end of 2002 and throughout 2003, there was a severe outbreak of infectious laryngotracheitis (ILT) in an intensive production area of commercial hens in the Sao Paulo State of Brazil. ILT virus was isolated from 28 flocks, and 21 isolates were genotyped by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) using four genes and eight restriction enzymes, and by partial sequencing of the infected cell protein 4 (ICP4) and thymidine kinase (TK) genes. Three groups resulted from the combinations of PCR-RFLP patterns: 19 field isolates formed Group I, and the remaining two isolates together with the chicken embryo origin (CEO) vaccine strains formed Group II. Group III comprised the tissue-culture origin (TCO) vaccine strain by itself. The PCR-RFLP results agreed with the sequencing results of two ICP4 gene fragments. The ICP4 gene sequence analysis showed that the 19 field isolates classified into Group I by RFLP-PCR were identical among themselves, but were different to the TCO and CEO vaccines. The two Group II isolates could not be distinguished from one of the CEO vaccines. The nucleotide and amino acid sequence analyses discriminated between the Brazilian and non-Brazilian isolates, as well as between the TCO and CEO vaccines. Sequence analysis of the TK gene enabled classification of the field isolates (Group I) as virulent and non-vaccine. This work shows that the severe ILT outbreak was caused by a highly virulent, non-vaccine strain.

Vertical Root Fracture in Upper Premolars with Endodontic Posts: Finite Element Analysis

Upper premolars restored with endodontic posts present a high incidence of vertical root fracture (VRF). Two hypotheses were tested: (1) the smaller mesiodistal diameter favors stress concentration in the root and (2) the lack of an effective bonding between root and post increases the risk of VRF. Using finite element analysis, maximum principal stress was analyzed in 3-dimensional intact upper second premolar models. From the intact models, new models were built including endodontic posts of different elastic modulus (E = 37 or E = 200 GPa) with circular or oval cross-section, either bonded or nonbonded to circular or oval cross-section root canals. The first hypothesis was partially confirmed because the conditions involving nonbonded, low-modulus posts showed lower tensile stress for oval canals compared to circular canals. Tensile stress peaks for the nonbonded models were approximately three times higher than for the bonded or intact models, therefore confirming the second hypothesis. (J Endod 2009;35:117-120)

Digital image correlation analysis of the load transfer by implant-supported restorations

This study compared splinted and non-splinted implant-supported prosthesis with and without a distal proximal contact using a digital image correlation method. An epoxy resin model was made with acrylic resin replicas of a mandibular first premolar and second molar and with threaded implants replacing the second premolar and first molar. Splinted and non-splinted metal-ceramic screw-retained crowns were fabricated and loaded with and without the presence of the second molar. A single-camera measuring system was used to record the in-plane deformation on the model surface at a frequency of 1.0 Hz under a load from 0 to 250 N. The images were then analyzed with specialist software to determine the direct (horizontal) and shear strains along the model. Not splinting the crowns resulted in higher stress transfer to the supporting implants when the second molar replica was absent. The presence of a second molar and an effective interproximal contact contributed to lower stress transfer to the supporting structures even for non-splinted restorations. Shear strains were higher in the region between the molars when the second molar was absent, regardless of splinting. The opposite was found for the region between the implants, which had higher shear strain values when the second molar was present. When an effective distal contact is absent, non-splinted implant-supported restorations introduce higher direct strains to the supporting structures under loading. Shear strains appear to be dependent also on the region within the model, with different regions showing different trends in strain changes in the absence of an effective distal contact. (C) 2011 Elsevier Ltd. All rights reserved.

Transcriptome analysis of nicotine-exposed cells from the brainstem of neonate spontaneously hypertensive and Wistar Kyoto rats

In this study, the effects of nicotine on global gene expression of cultured cells from the brainstem of spontaneously hypertensive rat (SHR) and normotensive Wistar Kyoto (WKY) rats were evaluated using whole-genome oligoarrays. We found that nicotine may act differentially on the gene expression profiles of SHR and WKY. The influence of strain was present in 321 genes that were differentially expressed in SHR as compared with WKY brainstem cells independently of the nicotine treatment. A total of 146 genes had their expression altered in both strains after nicotine exposure. Interaction between nicotine treatment and the strain was observed to affect the expression of 229 genes that participate in cellular pathways related to neurotransmitter secretion, intracellular trafficking and cell communication, and are possibly involved in the phenotypic differentiation between SHR and WKY rats, including hypertension. Further characterization of their function in hypertension development is warranted. The Pharmacogenomics Journal (2010) 10, 134-160; doi:10.1038/tpj.2009.42; published online 15 September 2009