The temperate Burkholderia phage AP3 of the Peduovirinae shows efficient antimicrobial activity against B. cenocepacia of the IIIA lineage

Burkholderia phage AP3 (vB_BceM_AP3) is a temperate virus of the Myoviridae and the Peduovirinae subfamily (P2likevirus genus). This phage specifically infects multidrug-resistant clinical Burkholderia cenocepacia lineage IIIA strains commonly isolated from cystic fibrosis patients. AP3 exhibits high pairwise nucleotide identity (61.7%) to Burkholderia phage KS5, specific to the same B. cenocepacia host, and has 46.7% - 49.5% identity to phages infecting other species of Burkholderia. The lysis cassette of these related phages has a similar organization (putative antiholin, putative holin, endolysin and spanins) and shows 29-98% homology between specific lysis genes, in contrast to Enterobacteria phage P2, the hallmark phage of this genus. The AP3 and KS5 lysis genes have conserved locations and high amino acid sequence similarity. The AP3 bacteriophage particles remain infective up to 5 h at pH 4-10 and are stable at 60°C for 30 min, but are sensitive to chloroform, with no remaining infective particles after 24 h of treatment. AP3 lysogeny can occur by stable genomic integration and by pseudo-lysogeny. The lysogenic bacterial mutants did not exhibit any significant changes in virulence compared to wild-type host strain when tested in the Galleria mellonella moth wax model. Moreover, AP3 treatment of larvae infected with B. cenocepacia revealed a significant increase (P < 0.0001) in larvae survival in comparison to AP3-untreated infected larvae. AP3 showed robust lytic activity, as evidenced by its broad host range, the absence of increased virulence in lysogenic isolates, the lack of bacterial gene disruption conditioned by bacterial tRNA downstream integration site, and the absence of detected toxin sequences. These data suggest the AP3 phage is a promising potent agent against bacteria belonging to most common B. cenocepacia IIIA lineage strains.

Characterization of entanglement transformation via group representation theory

Entanglement transformation of composite quantum systems is investigated in the context of group representation theory. Representation of the direct product group SL(2, C) circle times SL(2, C), composed of local operators acting on the binary composite system, is realized in the four-dimensional complex space in terms of a set of novel bases that are pseudo-orthonormalized. The two-to-one homomorphism is then established for the group SL(2, C) circle times SL(2, C) onto the SO(4, C). It is shown that the resulting representation theory leads to the complete characterization for the entanglement transformation of the binary composite system.

SYNTHESIS AND CRYSTAL-STRUCTURE OF (C9H7GDCL2.3THF)THF

The indenylpdolinium dichloride tristetrahydrofuranate (C9H7GdCl2.3THF)THF was prepared and its crystal structure (monoclinic space group P2(1)) determined by X-ray diffraction. In C9H7GdCl2.3THF, Gd, O(1), O(2), O(3) and the centroid of the five-membered indenyl ring form a plane, and Cl(1) and Cl(2) are located at two opposite sides of the plane to give a pseudo-octahedron. The coordination number of Gd is eight.

Substrats neuronaux de la mémoire épisodique et de la mémoire de travail dans le vieillissement normal et pathologique

La maladie d’Alzheimer (MA) est de loin le type de démence le plus répandu chez les personnes âgées. Il est maintenant possible de proposer un certain nombre d’interventions ou de stratégies préventives aux personnes portant un diagnostic de MA ou à risque de développer la maladie. Il est donc important de diagnostiquer cette maladie le plus tôt possible. Les personnes avec un trouble cognitif léger (TCL) représentent une population d’intérêt puisqu’elles sont à haut risque d’évoluer vers une démence et plusieurs d’entres elles seraient ainsi dans une phase prodromale de la MA. Les travaux de cette thèse visent à explorer les activations fonctionnelles associées à la mémoire épisodique et à la mémoire de travail dans le TCL ainsi qu’aux effets de la sévérité de la maladie et des caractéristiques de la tâche sur ces activations. Dans un premier temps, nous exposerons les connaissances relatives au niveau des atteintes cognitives, du patron d’activation fonctionnelle et des plus récents modèles élaborés pour expliquer les changements d’activation dans le vieillissement normal et pathologique (Chapitre 1). Par la suite, les études réalisées dans le cadre de cette thèse seront présentées. Nous avons d’abord étudié la fiabilité du signal d’activation chez les TCL et chez les personnes âgées saines (PA) à l’aide de tâches d’encodage et de récupération de mots (Chapitre 2). Nous avons ensuite comparé le patron d’activation cérébral des PA et des personnes TCL alors qu’elles réalisaient une tâche d’encodage et de récupération de mots. L’effet de la sévérité a été évalué en corrélant les activations des personnes TCL à leurs scores obtenu à une échelle évaluant leur cognition globale (Chapitre 3). L’effet de sévérité a ensuite été étudié de manière plus approfondie chez un plus grand nombre de TCL en utilisant la médiane du groupe à cette même échelle pour déterminer un groupe de TCL plus atteints et un groupe de TCL moins atteints. Ces deux groupes ont ensuite été comparés à un groupe de PA lors d’une tâche d’encodage de paires de mots reliés sémantiquement ou non-reliés (Chapitre 4), une tâche de reconnaissance de paires de mots mesurant principalement la familiarité ou principalement la recollection (Chapitre 5), ainsi que deux tâches impliquant des composantes différentes de la mémoire de travail et des fonctions exécutives, soit la manipulation de l’information et l’attention divisée (Chapitre 6). Les résultats présentés dans cette thèse ont mis en évidence une distinction entre le patron d’activation des TCL et des PA qui semble caractérisée par une interaction entre le niveau de sévérité de la maladie et les processus cognitifs impliqués dans la tâche. L’effet de sévérité a été observé lors de plusieurs tâches impliquant des processus cognitifs différents où les MCI moins atteints ont montré principalement des hyperactivations sous-tendant des mécanismes compensatoires et les MCI plus atteints ont montré principalement des hypoactivations soulignant la dégradation de ces mécanismes. Par ailleurs, les résultats de nos études ont aussi montré que cet effet de sévérité est modulé par le moment d’altération du processus cognitif impliqué dans la tâche: les processus altérés précocément dans le TCL sont caractériséees par des hyperactivations chez les TCL moins atteints tandis que les processus altérés plus tardivement ont plutôt élicité des hyperactivations chez les TCL plus atteints. Les implications de ces résultats, ainsi que les limites des études, sont discutés (Chapitre 7).

Phonological similarity effects without a phonological store: an individual differences model

The feature model of immediate memory (Nairne, 1990) is applied to an experiment testing individual differences in phonological confusions amongst a group (N=100) of participants performing a verbal memory test. By simulating the performance of an equivalent number of “pseudo-participants” the model fits both the mean performance and the variability within the group. Experimental data show that high-performing individuals are significantly more likely to demonstrate phonological confusions than low performance individuals and this is also true of the model, despite the model’s lack of either an explicit phonological store or a performance-linked strategy shift away from phonological storage. It is concluded that a dedicated phonological store is not necessary to explain the basic phonological confusion effect, and the reduction in such an effect can also be explained without requiring a change in encoding or rehearsal strategy or the deployment of a different storage buffer.

O que e o método científico: uma reflexão crítica sobre o método científico como subsídio para o ensino das ciências naturais

Ensinar ciência e, acima de tudo, ensinar o método científico e desenvolver a atitude crítica do estudante. Isto significa substituir a visão da ciência como uma coleção de fatos e teorias definitivamente estabelecidos, pela visão da ciência como um conhecimento racional - Porque crítico -, conjectural, provisório, sempre capaz de ser questionado e corrigido. Significa também opor à visão da ciência como uma representação completa e perfeita de fenômenos diretamente observáveis, a visão da ciência como uma reconstrução idealizada e parcial da realidade, que explica o visível pelo invisível. Nessa linha de raciocínio, devemos opor à idéia de uma observação pura e imparcial dos fatos, a ideia da observação guiada por hipóteses e teorias. Ensinar o meto do cientifico é questionar a ideia de que descobrimos e verificamos hipóteses através de procedimentos indutivos, substituindo-a pela ideia de que inventamos conjecturas ousadas, surgidas de nossa imaginação. Essas conjecturas, contudo, deverão ser testadas o mais severamente possível, através de tentativas de refutação que façam uso de experimentos controlados. No lugar da ilusória busca de teorias verificáveis, verdadeiras -ou pelo menos cada vez mais prováveis devemos buscar teorias de maior refutabilidade, cada vez mais amplas, precisas, profundas, de maior grau de corroboração e, talvez, mais próximas da verdade. Finalmente, ensinar o método científico significa também criticar cada uma das visões alternativas de ciência, propondo novos critérios para avaliar hipóteses e teorias científicas. É desnecessário dizer que estes critérios, por sua vez, devem também ser criticados, visto que a ausência de discussão crítica e a aceitação passiva e dogmática de um conjunto de ideias ou teorias e a não ciência, a pseudociência, enfim, a negação do espírito crítico e da racionalidade do homem.

Nitrogênio e potássio em bananeira via fertirrigação e adubação convencional-atributos químicos do solo

Realizou-se um experimento em Pindorama (SP), no qual se avaliaram os efeitos da fertirrigação e da adubação convencional com N e K em alguns atributos químicos de solo sob cultivo com bananeira, durante dois ciclos de produção. Avaliaram-se a disponibilidade e a movimentação de nutrientes (P, K, Ca e Mg) no perfil do solo, bem como outros atributos químicos (matéria orgânica, acidez e saturação por bases), por meio de amostragens realizadas na implantação do experimento e ao final do primeiro e segundo ciclos de produção. Os principais efeitos dos tratamentos foram no pH do solo e no teor de K+ trocável. A adubação, tanto aplicada via fertirrigação como na forma convencional, implicou incrementos na acidez do solo, principalmente até 20 cm de profundidade. Observou-se que o impacto da adubação via fertirrigação no pH do solo foi proporcional à dose. A adubação convencional também causou decréscimo no pH, especialmente na região mais próxima das plantas, refletindo o efeito da aplicação localizada dos fertilizantes. A aplicação de adubo sólido na superfície do solo determinou significativo acúmulo de K nas camadas até 20 cm e na região mais próxima ao pseudocaule das plantas. Os efeitos da adubação via fertirrigação foram mais difusos, visto que os adubos são espalhados numa área de solo maior do que a coberta pela adubação convencional.

Geração de casos de teste a partir de especificações B

With the increasing complexity of software systems, there is also an increased concern about its faults. These faults can cause financial losses and even loss of life. Therefore, we propose in this paper the minimization of faults in software by using formally specified tests. The combination of testing and formal specifications is gaining strength in searches mainly through the MBT (Model-Based Testing). The development of software from formal specifications, when the whole process of refinement is done rigorously, ensures that what is specified in the application will be implemented. Thus, the implementation generated from these specifications would accurately depict what was specified. But not always the specification is refined to the level of implementation and code generation, and in these cases the tests generated from the specification tend to find fault. Additionally, the generation of so-called "invalid tests", ie tests that exercise the application scenarios that were not addressed in the specification, complements more significantly the formal development process. Therefore, this paper proposes a method for generating tests from B formal specifications. This method was structured in pseudo-code. The method is based on the systematization of the techniques of black box testing of boundary value analysis, equivalence partitioning, as well as the technique of orthogonal pairs. The method was applied to a B specification and B test machines that generate test cases independent of implementation language were generated. Aiming to validate the method, test cases were transformed manually in JUnit test cases and the application, created from the B specification and developed in Java, was tested. Faults were found with the execution of the JUnit test cases

Can a Strychnos species be used as antiulcer agent? Ulcer healing action from alkaloid fraction of Strychnos pseudoquina St. Hil. (Loganiaceae)

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

Avaliação das dimensões e relacionamentos dos arcos dentários no tratamento da má-oclusão classe II, divisão 1 de Angle com aparelho bionator de Balters

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Condições de otimalidade para controle ótimo via formalismo de Dubovitskii-Milyutin

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Application of reactive fluid transport modeling to hydrothermal systems

A one-dimensional multi-component reactive fluid transport algorithm, 1DREACT (Steefel, 1993) was used to investigate different fluid-rock interaction systems. A major short coming of mass transport calculations which include mineral reactions is that solid solutions occurring in many minerals are not treated adequately. Since many thermodynamic models of solid solutions are highly non-linear, this can seriously impact on the stability and efficiency of the solution algorithms used. Phase petrology community saw itself faced with a similar predicament 10 years ago. To improve performance and reliability, phase equilibrium calculations have been using pseudo compounds. The same approach is used here in the first, using the complex plagioclase solid solution as an example. Thermodynamic properties of a varying number of intermediate plagioclase phases were calculated using ideal molecular, Al-avoidance, and non-ideal mixing models. These different mixing models can easily be incorporated into the simulations without modification of the transport code. Simulation results show that as few as nine intermediate compositions are sufficient to characterize the diffusional profile between albite and anorthite. Hence this approach is very efficient, and can be used with little effort. A subsequent chapter reports the results of reactive fluid transport modeling designed to constrain the hydrothermal alteration of Paleoproterozoic sediments of the Southern Lake Superior region. Field observations reveal that quartz-pyrophyllite (or kaolinite) bearing assemblages have been transformed into muscovite-pyrophyllite-diaspore bearing assemblages due to action of fluids migrating along permeable flow channels. Fluid-rock interaction modeling with an initial qtz-prl assemblage and a K-rich fluid simulates the formation of observed mineralogical transformation. The bulk composition of the system evolves from an SiO2-rich one to an Al2O3+K2O-rich one. Simulations show that the fluid flow was up-temperature (e.g. recharge) and that fluid was K-rich. Pseudo compound approach to include solid solutions in reactive transport models was tested in modeling hydrothermal alteration of Icelandic basalts. Solid solutions of chlorites, amphiboles and plagioclase were included as the secondary mineral phases. Saline and fresh water compositions of geothermal fluids were used to investigate the effect of salinity on alteration. Fluid-rock interaction simulations produce the observed mineral transformations. They show that roughly the same alteration minerals are formed due to reactions with both types of fluid which is in agreement with the field observations. A final application is directed towards the remediation of nitrate rich groundwaters. Removal of excess nitrate from groundwater by pyrite oxidation was modeled using the reactive fluid transport algorithm. Model results show that, when a pyrite-bearing, permeable zone is placed in the flow path, nitrate concentration in infiltrating water can be significantly lowered, in agreement with proposals from the literature. This is due to nitrogen reduction. Several simulations investigate the efficiency of systems with different mineral reactive surface areas, reactive barrier zone widths, and flow rates to identify the optimum setup.

Three New Methods for Computing Subresultant Polynomial Remainder Sequences (PRS’S)

Given the polynomials f, g ∈ Z[x] of degrees n, m, respectively, with n > m, three new, and easy to understand methods — along with the more efficient variants of the last two of them — are presented for the computation of their subresultant polynomial remainder sequence (prs). All three methods evaluate a single determinant (subresultant) of an appropriate sub-matrix of sylvester1, Sylvester’s widely known and used matrix of 1840 of dimension (m + n) × (m + n), in order to compute the correct sign of each polynomial in the sequence and — except for the second method — to force its coefficients to become subresultants. Of interest is the fact that only the first method uses pseudo remainders. The second method uses regular remainders and performs operations in Q[x], whereas the third one triangularizes sylvester2, Sylvester’s little known and hardly ever used matrix of 1853 of dimension 2n × 2n. All methods mentioned in this paper (along with their supporting functions) have been implemented in Sympy and can be downloaded from the link http://inf-server.inf.uth.gr/~akritas/publications/subresultants.py

The role of non-factorizability in determining "pseudo-classical" non-separability

This article introduces a “pseudo classical” notion of modelling non-separability. This form of non-separability can be viewed as lying between separability and quantum-like non-separability. Non-separability is formalized in terms of the non-factorizabilty of the underlying joint probability distribution. A decision criterium for determining the non-factorizability of the joint distribution is related to determining the rank of a matrix as well as another approach based on the chi-square-goodness-of-fit test. This pseudo-classical notion of non-separability is discussed in terms of quantum games and concept combinations in human cognition.

Pseudo-merohedral twinning in the structure of the hydrated 1:1 proton-transfer compound of 5-sulfosalicylic acid with 4-aminopyridine

The structure of the pseudo-merohedrally twinned crystal of the 1:1 proton-transfer compound of 5-sulfosalicylic acid (3-carboxy-4-hydroxybenzenesulfonic acid) with 4-aminopyridine: 4-aminopyridinium 3-carboxy-4-hydroxybenzenesulfonate sesquihydrate has been determined at 180 K and the hydrogen-bonding pattern is described. Crystals of the compound are monoclinic with space group P21/c, with unit cell dimensions a = 35.2589(8), b = 7.1948(1), c = 24.5851(5) Å, β = 110.373(2)o, and Z = 16. The monoclinic asymmetric unit comprises four cation-anion pairs and six water molecules of solvation with only the pyridinium cations having pseudo-symmetry as a result of inter-cation aromatic ring π-π stacking effects. Extensive hydrogen bonding gives a three-dimensional framework structure.