Modelling adhesive joints with cohesive zone models: effect of the cohesive law shape of the adhesive layer

Adhesively-bonded joints are extensively used in several fields of engineering. Cohesive Zone Models (CZM) have been used for the strength prediction of adhesive joints, as an add-in to Finite Element (FE) analyses that allows simulation of damage growth, by consideration of energetic principles. A useful feature of CZM is that different shapes can be developed for the cohesive laws, depending on the nature of the material or interface to be simulated, allowing an accurate strength prediction. This work studies the influence of the CZM shape (triangular, exponential or trapezoidal) used to model a thin adhesive layer in single-lap adhesive joints, for an estimation of its influence on the strength prediction under different material conditions. By performing this study, guidelines are provided on the possibility to use a CZM shape that may not be the most suited for a particular adhesive, but that may be more straightforward to use/implement and have less convergence problems (e.g. triangular shaped CZM), thus attaining the solution faster. The overall results showed that joints bonded with ductile adhesives are highly influenced by the CZM shape, and that the trapezoidal shape fits best the experimental data. Moreover, the smaller is the overlap length (LO), the greater is the influence of the CZM shape. On the other hand, the influence of the CZM shape can be neglected when using brittle adhesives, without compromising too much the accuracy of the strength predictions

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

<p>Abstract</p> <p>Background</p> <p><it>Xylella fastidiosa</it>, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, <it>X. fastidiosa </it>needs to cope with nitrogen limitation in its natural habitat.</p> <p>Results</p> <p>In this work, we performed a whole-genome microarray analysis of the <it>X. fastidiosa </it>nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the <it>rpoN </it>null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ⁵⁴-dependent manner. A more complete picture of the σ⁵⁴regulon was achieved by combining the transcriptome data with an <it>in silico </it>search for potential σ⁵⁴-dependent promoters, using a position weight matrix approach. One of these σ⁵⁴-predicted binding sites, located upstream of the <it>glnA </it>gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ⁵⁴-dependent promoter.</p> <p>Conclusions</p> <p>Together, these results show that nitrogen starvation causes intense changes in the <it>X. fastidiosa </it>transcriptome and some of these differentially expressed genes belong to the σ⁵⁴regulon.</p

Fur controls iron homeostasis and oxidative stress defense in the oligotrophic alpha-proteobacterium Caulobacter crescentus

In most bacteria, the ferric uptake regulator (Fur) is a global regulator that controls iron homeostasis and other cellular processes, such as oxidative stress defense. In this work, we apply a combination of bioinformatics, in vitro and in vivo assays to identify the Caulobacter crescentus Fur regulon. A C. crescentus fur deletion mutant showed a slow growth phenotype, and was hypersensitive to H2O2 and organic peroxide. Using a position weight matrix approach, several predicted Fur-binding sites were detected in the genome of C. crescentus, located in regulatory regions of genes not only involved in iron uptake and usage but also in other functions. Selected Fur-binding sites were validated using electrophoretic mobility shift assay and DNAse I footprinting analysis. Gene expression assays revealed that genes involved in iron uptake were repressed by iron-Fur and induced under conditions of iron limitation, whereas genes encoding iron-using proteins were activated by Fur under conditions of iron sufficiency. Furthermore, several genes that are regulated via small RNAs in other bacteria were found to be directly regulated by Fur in C. crescentus. In conclusion, Fur functions as an activator and as a repressor, integrating iron metabolism and oxidative stress response in C. crescentus

Fur controls iron homeostasis and oxidative stress defense in the oligotrophic alpha-proteobacterium Caulobacter crescentus

In most bacteria, the ferric uptake regulator (Fur) is a global regulator that controls iron homeostasis and other cellular processes, such as oxidative stress defense. In this work, we apply a combination of bioinformatics, in vitro and in vivo assays to identify the Caulobacter crescentus Fur regulon. A C. crescentus fur deletion mutant showed a slow growth phenotype, and was hypersensitive to H2O2 and organic peroxide. Using a position weight matrix approach, several predicted Fur-binding sites were detected in the genome of C. crescentus, located in regulatory regions of genes not only involved in iron uptake and usage but also in other functions. Selected Fur-binding sites were validated using electrophoretic mobility shift assay and DNAse I footprinting analysis. Gene expression assays revealed that genes involved in iron uptake were repressed by iron-Fur and induced under conditions of iron limitation, whereas genes encoding iron-using proteins were activated by Fur under conditions of iron sufficiency. Furthermore, several genes that are regulated via small RNAs in other bacteria were found to be directly regulated by Fur in C. crescentus. In conclusion, Fur functions as an activator and as a repressor, integrating iron metabolism and oxidative stress response in C. crescentus

Global transcriptional response of Caulobacter crescentus to iron availability

Abstract\ud \ud \ud \ud Background\ud In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown.\ud \ud \ud \ud Results\ud In this work we report the identification of iron-responsive and Fur-regulated genes in C. crescentus using microarray-based global transcriptional analyses. We identified 42 genes that were strongly upregulated both by mutation of fur and by iron limitation condition. Among them, there are genes involved in iron uptake (four TonB-dependent receptor gene clusters, and feoAB), riboflavin biosynthesis and genes encoding hypothetical proteins. Most of these genes are associated with predicted Fur binding sites, implicating them as direct targets of Fur-mediated repression. These data were validated by β-galactosidase and EMSA assays for two operons encoding putative transporters. The role of Fur as a positive regulator is also evident, given that 27 genes were downregulated both by mutation of fur and under low-iron condition. As expected, this group includes many genes involved in energy metabolism, mostly iron-using enzymes. Surprisingly, included in this group are also TonB-dependent receptors genes and the genes fixK, fixT and ftrB encoding an oxygen signaling network required for growth during hypoxia. Bioinformatics analyses suggest that positive regulation by Fur is mainly indirect. In addition to the Fur modulon, iron limitation altered expression of 113 more genes, including induction of genes involved in Fe-S cluster assembly, oxidative stress and heat shock response, as well as repression of genes implicated in amino acid metabolism, chemotaxis and motility.\ud \ud \ud \ud Conclusions\ud Using a global transcriptional approach, we determined the C. crescentus iron stimulon. Many but not all of iron responsive genes were directly or indirectly controlled by Fur. The iron limitation stimulon overlaps with other regulatory systems, such as the RpoH and FixK regulons. Altogether, our results showed that adaptation of C. crescentus to iron limitation not only involves increasing the transcription of iron-acquisition systems and decreasing the production of iron-using proteins, but also includes novel genes and regulatory mechanisms.We are grateful to Michael T. Laub for making the C. crescentus DNA microarray slides available and Carla Rosenberg lab for assistance with the microarray scanning. This work was supported by grant 470663/2011-1 from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). During the course of this work, JFSN and RFL were supported by postdoctoral fellowships, grants 2007/56306-0 and 2008/52874-6, from São Paulo Research Foundation (FAPESP). MVM is partly supported by CNPq.We are grateful to Michael T. Laub for making the C. crescentus DNA microarray slides available and Carla Rosenberg lab for assistance with the microarray scanning. This work was supported by grant 470663/20111 from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). During the course of this work, JFSN and RFL were supported by postdoctoral fellowships, grants 2007/563060 and 2008/528746, from São Paulo Research Foundation (FAPESP). MVM is partly supported by CNPq

Trajectory Modeling via Random Utility Inverse Reinforcement Learning

We consider the problem of modeling trajectories of drivers in a road network from the perspective of inverse reinforcement learning. Cars are detected by sensors placed on sparsely distributed points on the street network of a city. As rational agents, drivers are trying to maximize some reward function unknown to an external observer. We apply the concept of random utility from econometrics to model the unknown reward function as a function of observed and unobserved features. In contrast to current inverse reinforcement learning approaches, we do not assume that agents act according to a stochastic policy; rather, we assume that agents act according to a deterministic optimal policy and show that randomness in data arises because the exact rewards are not fully observed by an external observer. We introduce the concept of extended state to cope with unobserved features and develop a Markov decision process formulation of drivers decisions. We present theoretical results which guarantee the existence of solutions and show that maximum entropy inverse reinforcement learning is a particular case of our approach. Finally, we illustrate Bayesian inference on model parameters through a case study with real trajectory data from a large city in Brazil.Comment: 31 pages; expanded version, with the addition of proofs not present in the first versio

Canopy Height and Its Relationship with Leaf Area Index and Light Interception of Tropical Grasses

Photosynthetic tissues, mainly green leaves, are the major component of forage growth and development. The amount of these tissues in a forage plant is influenced directly by the cutting management, which is based on cutting frequency and stubble height. It is usual to recommend as a management practice to cut (or graze) the forage whenever it reaches a given stubble height. Brougham (1956) stated that, when the forage canopy is intercepting 95% of the photosynthetic active radiation, this is the critical leaf area index (LAI), which means the forage is near its maximum growth rate without shading itself. There is also the optimum LAI, where the forage reaches the maximum point of mass accumulation, indicating time to start grazing or cut. Generally the critical and optimum LAI have close values, but they are not necessarily the same (Brown and Blaser, 1968). This trial evaluated the relationship among canopy height, leaf area index, and light interception in ten different tropical grasses

EmrR-Dependent Upregulation of the Efflux Pump EmrCAB Contributes to Antibiotic Resistance in Chromobacterium violaceum

Chromobacterium violaceum is an environmental Gram-negative bacterium that causes infections in humans. Treatment of C. violaceum infections is difficult and little is known about the mechanisms of antibiotic resistance in this bacterium. In this work, we identified mutations in the MarR family transcription factor EmrR and in the protein GyrA as key determinants of quinolone resistance in C. violaceum, and we defined EmrR as a repressor of the MFS-type efflux pump EmrCAB. Null deletion of emrR caused increased resistance to nalidixic acid, but not to other quinolones or antibiotics of different classes. Moreover, the ΔemrR mutant showed decreased production of the purple pigment violacein. Importantly, we isolated C. violaceum spontaneous nalidixic acid-resistant mutants with a point mutation in the DNA-binding domain of EmrR (R92H), with antibiotic resistance profile similar to that of the ΔemrR mutant. Other spontaneous mutants with high MIC values for nalidixic acid and increased resistance to fluoroquinolones presented point mutations in the gene gyrA. Using DNA microarray, Northern blot and EMSA assays, we demonstrated that EmrR represses directly a few dozen genes, including the emrCAB operon and other genes related to transport, oxidative stress and virulence. This EmrR repression on emrCAB was relieved by salicylate. Although mutation of the C. violaceum emrCAB operon had no effect in antibiotic susceptibility or violacein production, deletion of emrCAB in an emrR mutant background restored antibiotic susceptibility and violacein production in the ΔemrR mutant. Using a biosensor reporter strain, we demonstrated that the lack of pigment production in ΔemrR correlates with the accumulation of quorum-sensing molecules in the cell supernatant of this mutant strain. Therefore, our data revealed that overexpression of the efflux pump EmrCAB via mutation and/or derepression of EmrR confers quinolone resistance and alters quorum-sensing signaling in C. violaceum, and that point mutation in emrR can contribute to emergence of antibiotic resistance in bacteria

Pharmaceutical development of paracetamol oral suspension

The aims of this work are obtaining and evaluating paracetamol oral suspension 32 mg/mL by qualitative and quantitative planning of the ingredients. The observations of the physical-chemical formulations were based in comparison with the specifications of paracetamol solution contained in the Brazilian Pharmacopoeia and editing with some analysis on the same reference drug (Tylenol® child 32 mg / mL). We sought to develop a low cost and good quality formulation, acceptable to the children's market, since the suspension dosage form is characterized by disguising the unpleasant taste of drugs. The chosen formulation showed good rheology properties, excellent sensory and values of pH, viscosity, density and content within the pharmacopoeia specifications. We obtained a satisfactory formulation, with smaller amount of excipients in relation to the reference product, which can be used by diabetics and is compatible with the official specifications, with respect to physical-chemical tests performed.Colegio de Farmacéuticos de la Provincia de Buenos Aire

Effects of high intensity interval training on neuro-cardiovascular dynamic changes and mitochondrial dysfunction induced by high-fat diet in rats

This research was supported by the Brazilian National Council for Scientific and Technologic Development (CNPq) (Grant number: 474116/2008-5) and Carlos Chagas Filho Foundation for Research Support in the State of Rio de Janeiro (FAPERJ) (Grant number: E-26/ 111.732/2011), both received by Eliete Bouskela. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD