The canonical structure of Podolsky's generalized electrodynamics on the null-plane

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A molecular mechanism for Lys(49)-phospholipase A(2) activity based on ligand-induced conformational change

Agkistrodon contortrix laticinctus myotoxin is a Lys(49)- phospholipase A(2) (EC 3.1.1.4) isolated from the venom of the serpent A contortrix laticinctus (broad-banded copperhead). We present here three monomeric crystal structures of the myotoxin, obtained under different crystallization conditions. The three forms present notable structural differences and reveal that the presence of a ligand in the active site (naturally presumed to be a fatty acid) induces the exposure of a hydrophobic surface (the hydrophobic knuckle) toward the C terminus. The knuckle in A contortrix laticinctus myotoxin involves the side chains of Phe(121) and Phe(124) and is a consequence of the formation of a canonical structure for the main chain within the region of residues 118-125. Comparison with other Lys(49)-phospholipase A(2) myotoxins shows that although the knuckle is a generic structural motif common to all members of the family, it is not readily recognizable by simple sequence analyses. An activation mechanism is proposed that relates fatty acid retention at the active site to conformational changes within the C-terminal region, a part of the molecule that has long been associated with Ca2+-independent membrane damaging activity and myotoxicity. This provides, for the first time, a direct structural connection between the phospholipase active site and the C-terminal myotoxic site, justifying the otherwise enigmatic conservation of the residues of the former in supposedly catalytically inactive molecules.

Podolsky's electromagnetic theory on the null-plane

We have analyzed the null-plane canonical structure of Podolsky's electromagnetic theory. As a theory that contains higher order derivatives in the Lagrangian function, it was necessary to redefine the canonical momenta related to the field variables. We were able to find a set of first and second-class constraints, and also to derive the field equations of the system. Copyright © owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike Licence.

Implementação e testes de campo de um ESP digital

Neste trabalho é apresentado o desenvolvimento e os resultados da implementação e testes em campo de um estabilizador de sistema de potência (ESP) projetado com técnica de controle digital para fins de amortecimento de modos de oscilação eletromecânica observáveis em sinais de potência elétrica medido em uma unidade hidro-geradora, de 350 MVA da Usina Hidrelétrica de Tucuruí. É apresentada e aplicada a metodologia de identificação de modelos paramétricos lineares do tipo auto regressivo com entradas exógenas (ARX), para estimação de modelos com capacidade de capturar a informação relevante (amortecimento e freqüência natural) dos modos eletromecânicos dominantes do sistema. De posse do modelo paramétrico ARX, é efetuada então a síntese da lei de controle digital amortecedor para o ESP, através da técnica de deslocamento radial dos pólos da função de transferência de malha fechada. Para a síntese da lei de controle digital, utilizou-se uma estrutura canônica do tipo RST. Para os testes de campo, a lei de controle amortecedor do ESP digital foi codificada em linguagem C e embarcada em um protótipo cujo hardware é baseado em microcontrolador modelo DSPIC 30F3014, o qual incorpora um grande número de periféricos para aquisição e comunicação de dados. Para avaliar o desempenho do ESP digital desenvolvido, testes experimentais foram realizados em uma unidade geradora de 350 MVA da casa de força número 1, da UHE de Tucuruí. O estabilizador desenvolvido atua através da modulação da referência de tensão do regulador automático de tensão da respectiva unidade geradora, de acordo com as oscilações observadas através da medida de potência elétrica no estator do gerador. Os resultados de testes de campo mostraram um excelente desempenho do ESP digital no amortecimento de um modo eletromecânico, de freqüência natural de aproximadamente 1,7 Hz, observado nos teste de campo realizado.

Investigação de estratégias de controle digital para regulação de velocidade e emulação da dinâmica de turbinas hidráulicas, com implementação e testes experimentais em uma micromáquina de 10 KVA

Devido não ser comum o estudo de sistemas de potência em plantas reais como usinas hidrelétricas por causa dos riscos e custos que envolvem sua operação, dá-se preferência pela realização computacional de modelos matemáticos desse tipo de planta na resolução de problemas, desenvolvimento de novas tecnologias e formação de recursos humanos. No entanto, modelos realizados computacionalmente não proveem a experiência, visual, auditiva e tátil que um modelo físico real pode oferecer. Portanto, neste trabalho, apresenta-se a descrição e a modelagem de um sistema de geração em escala reduzida de 10kVA, que é um sistema físico real, composto por um motor CC, um gerador síncrono e transformadores, chamado também de sistema micromáquina, o qual faz parte da infraestrutura do Laboratório de Engenharia Elétrica da UFPA. Para este sistema, por intermédio deste trabalho de mestrado e do trabalho de mestrado de Moraes (2011), foram desenvolvido subsistemas eletrônicos e computacionais de acionamento, automação e controle para operá-lo de forma segura resultando em uma excelente plataforma didática para dar suporte às pesquisas em dinâmica e controle de sistemas de potência, bem como o desenvolvimento de trabalhos acadêmicos e de ensino. Nesse mesmo contexto, é apresentada uma proposta de técnica de emulação de turbina hidráulica, tendo como base o controle de potência aplicado ao motor CC do sistema micromáquina. Tal técnica foi desenvolvida principalmente com o propósito de dar suporte ao estudo e desenvolvimento de técnicas de regulação de velocidade de turbinas hidráulicas. Consequentemente, também é apresenta uma proposta de um regulador de velocidade digital para turbinas hidráulicas baseado na estrutura canônica RST de controle digital, cujos parâmetros são projetados por duas técnicas de projeto estudadas neste trabalho: o método de alocação polinomial de polos e o projeto de compensadores por atraso de fase pelo método de resposta em frequência para sistemas discretos. Logo para comprovar a eficácia das ferramentas de hardware, software e teóricas desenvolvidas neste trabalho, resultados de experimentos realizados no sistema micromáquina são apresentados e analisados.

On the Deactivation Mechanisms of Adenine-Thymine Base Pair

In this contribution, the multiconfigurational second-order perturbation theory method based on a complete active space reference wave function (CASSCF/CASPT2) is applied to study all possible single and double proton/hydrogen transfers between the nucleobases in the adenine-thymine (AT) base pair, analyzing the role of excited states with different nature [localized (LE) and charge transfer (CT)] and considering concerted as well as step-wise mechanisms. According to the findings, once the lowest excited states, localized in adenine, are populated during UV irradiation of the Watson-Crick base pair, the proton transfer in the N-O bridge does not require high energy in order to populate a CT state. The latter state will immediately relax toward a crossing with the ground state, which will funnel the system to either the canonical structure or the imino-enol tautomer. The base pair is also capable of repairing itself easily since the imino-enol species is unstable to thermal conversion.

Relative Affine Structure: Canonical Model for 3D from 2D Geometry and Applications

We propose an affine framework for perspective views, captured by a single extremely simple equation based on a viewer-centered invariant we call "relative affine structure". Via a number of corollaries of our main results we show that our framework unifies previous work --- including Euclidean, projective and affine --- in a natural and simple way, and introduces new, extremely simple, algorithms for the tasks of reconstruction from multiple views, recognition by alignment, and certain image coding applications.

Transposable elements: structure and dynamic of the autonomous retrotransposon R2 in Arthropoda with non-canonical reproduction

Eukaryotic ribosomal DNA constitutes a multi gene family organized in a cluster called nucleolar organizer region (NOR); this region is composed usually by hundreds to thousands of tandemly repeated units. Ribosomal genes, being repeated sequences, evolve following the typical pattern of concerted evolution. The autonomous retroelement R2 inserts in the ribosomal gene 28S, leading to defective 28S rDNA genes. R2 element, being a retrotransposon, performs its activity in the genome multiplying its copy number through a “copy and paste” mechanism called target primed reverse transcription. It consists in the retrotranscription of the element’s mRNA into DNA, then the DNA is integrated in the target site. Since the retrotranscription can be interrupted, but the integration will be carried out anyway, truncated copies of the element will also be present in the genome. The study of these truncated variants is a tool to examine the activity of the element. R2 phylogeny appears, in general, not consistent with that of its hosts, except some cases (e.g. Drosophila spp. and Reticulitermes spp.); moreover R2 is absent in some species (Fugu rubripes, human, mouse, etc.), while other species have more R2 lineages in their genome (the turtle Mauremys reevesii, the Japanese beetle Popilia japonica, etc). R2 elements here presented are isolated in 4 species of notostracan branchiopods and in two species of stick insects, whose reproductive strategies range from strict gonochorism to unisexuality. From sequencing data emerges that in Triops cancriformis (Spanish gonochoric population), in Lepidurus arcticus (two putatively unisexual populations from Iceland) and in Bacillus rossius (gonochoric population from Capalbio) the R2 elements are complete and encode functional proteins, reflecting the general features of this family of transposable elements. On the other hand, R2 from Italian and Austrian populations of T. cancriformis (respectively unisexual and hermaphroditic), Lepidurus lubbocki (two elements within the same Italian population, gonochoric but with unfunctional males) and Bacillus grandii grandii (gonochoric population from Ponte Manghisi) have sequences that encode incomplete or non-functional proteins in which it is possible to recognize only part of the characteristic domains. In Lepidurus couesii (Italian gonochoric populations) different elements were found as in L. lubbocki, and the sequencing is still in progress. Two hypothesis are given to explain the inconsistency of R2/host phylogeny: vertical inheritance of the element followed by extinction/diversification or horizontal transmission. My data support previous study that state the vertical transmission as the most likely explanation; nevertheless horizontal transfer events can’t be excluded. I also studied the element’s activity in Spanish populations of T. cancriformis, in L. lubbocki, in L. arcticus and in gonochoric and parthenogenetic populations of B. rossius. In gonochoric populations of T. cancriformis and B. rossius I found that each individual has its own private set of truncated variants. The situation is the opposite for the remaining hermaphroditic/parthenogenetic species and populations, all individuals sharing – in the so far analyzed samples - the majority of variants. This situation is very interesting, because it isn’t concordant with the Muller’s ratchet theory that hypothesizes the parthenogenetic populations being either devoided of transposable elements or TEs overloaded. My data suggest a possible epigenetic mechanism that can block the retrotransposon activity, and in this way deleterious mutations don’t accumulate.

Adsorption of Supercritical fluids on graphitised thermal carbon black: Molecular layer structure theory versus grand canonical Monte Carlo simulation

This paper presents a detailed analysis of adsorption of supercritical fluids on nonporous graphitized thermal carbon black. Two methods are employed in the analysis. One is the molecular layer structure theory (MLST), proposed recently by our group, and the other is the grand canonical Monte Carlo (GCMC) simulation. They were applied to describe the adsorption of argon, krypton, methane, ethylene, and sulfur hexafluoride on graphitized thermal carbon black. It was found that the MLST describes all the experimental data at various temperatures well. Results from GCMC simulations describe well the data at low pressure but show some deviations at higher pressures for all the adsorbates tested. The question of negative surface excess is also discussed in this paper.

Spherical image-based visual servo and structure estimation

This paper presents a formulation of image-based visual servoing (IBVS) for a spherical camera where coordinates are parameterized in terms of colatitude and longitude: IBVSSph. The image Jacobian is derived and simulation results are presented for canonical rotational, translational as well as general motion. Problems with large rotations that affect the planar perspective form of IBVS are not present on the sphere, whereas the desirable robustness properties of IBVS are shown to be retained. We also describe a structure from motion (SfM) system based on camera-centric spherical coordinates and show how a recursive estimator can be used to recover structure. The spherical formulations for IBVS and SfM are particularly suitable for platforms, such as aerial and underwater robots, that move in SE(3).

Graph rigidity for near-coplanar structure from motion

Recent algorithms for monocular motion capture (MoCap) estimate weak-perspective camera matrices between images using a small subset of approximately-rigid points on the human body (i.e. the torso and hip). A problem with this approach, however, is that these points are often close to coplanar, causing canonical linear factorisation algorithms for rigid structure from motion (SFM) to become extremely sensitive to noise. In this paper, we propose an alternative solution to weak-perspective SFM based on a convex relaxation of graph rigidity. We demonstrate the success of our algorithm on both synthetic and real world data, allowing for much improved solutions to marker less MoCap problems on human bodies. Finally, we propose an approach to solve the two-fold ambiguity over bone direction using a k-nearest neighbour kernel density estimator.

Population structure of Bactrocera dorsalis s.s., B. papayae and B. philippinensis (Diptera: Tephritidae) in southeast Asia: evidence for a single species hypothesis using mitochondrial DNA and wingshape data

Background Bactrocera dorsalis s.s. is a pestiferous tephritid fruit fly distributed from Pakistan to the Pacific, with the Thai/Malay peninsula its southern limit. Sister pest taxa, B. papayae and B. philippinensis, occur in the southeast Asian archipelago and the Philippines, respectively. The relationship among these species is unclear due to their high molecular and morphological similarity. This study analysed population structure of these three species within a southeast Asian biogeographical context to assess potential dispersal patterns and the validity of their current taxonomic status. Results Geometric morphometric results generated from 15 landmarks for wings of 169 flies revealed significant differences in wing shape between almost all sites following canonical variate analysis. For the combined data set there was a greater isolation-by-distance (IBD) effect under a ‘non-Euclidean’ scenario which used geographical distances within a biogeographical ‘Sundaland context’ (r2 = 0.772, P < 0.0001) as compared to a ‘Euclidean’ scenario for which direct geographic distances between sample sites was used (r2 = 0.217, P < 0.01). COI sequence data were obtained for 156 individuals and yielded 83 unique haplotypes with no correlation to current taxonomic designations via a minimum spanning network. BEAST analysis provided a root age and location of 540kya in northern Thailand, with migration of B. dorsalis s.l. into Malaysia 470kya and Sumatra 270kya. Two migration events into the Philippines are inferred. Sequence data revealed a weak but significant IBD effect under the ‘non-Euclidean’ scenario (r2 = 0.110, P < 0.05), with no historical migration evident between Taiwan and the Philippines. Results are consistent with those expected at the intra-specific level. Conclusions Bactrocera dorsalis s.s., B. papayae and B. philippinensis likely represent one species structured around the South China Sea, having migrated from northern Thailand into the southeast Asian archipelago and across into the Philippines. No migration is apparent between the Philippines and Taiwan. This information has implications for quarantine, trade and pest management.

The sphynx's new riddle : how to relate the canonical formula of myth to quantum interaction

We introduce Claude Lévi Strauss' canonical formula (CF), an attempt to rigorously formalise the general narrative structure of myth. This formula utilises the Klein group as its basis, but a recent work draws attention to its natural quaternion form, which opens up the possibility that it may require a quantum inspired interpretation. We present the CF in a form that can be understood by a non-anthropological audience, using the formalisation of a key myth (that of Adonis) to draw attention to its mathematical structure. The future potential formalisation of mythological structure within a quantum inspired framework is proposed and discussed, with a probabilistic interpretation further generalising the formula

Structure informationnelle et constructions du kabyle : Etude de trois types de phrase dans le cadre de la grammaire constructionnelle

Information structure and Kabyle constructions Three sentence types in the Construction Grammar framework The study examines three Kabyle sentence types and their variants. These sentence types have been chosen because they code the same state of affairs but have different syntactic structures. The sentence types are Dislocated sentence, Cleft sentence, and Canonical sentence. I argue first that a proper description of these sentence types should include information structure and, second, that a description which takes into account information structure is possible in the Construction Grammar framework. The study thus constitutes a testing ground for Construction Grammar for its applicability to a less known language. It constitutes a testing ground notably because the differentiation between the three types of sentences cannot be done without information structure categories and, consequently, these categories must be integrated also in the grammatical description. The information structure analysis is based on the model outlined by Knud Lambrecht. In that model, information structure is considered as a component of sentence grammar that assures the pragmatically correct sentence forms. The work starts by an examination of the three sentence types and the analyses that have been done in André Martinet s functional grammar framework. This introduces the sentence types chosen as the object of study and discusses the difficulties related to their analysis. After a presentation of the state of the art, including earlier and more recent models, the principles and notions of Construction Grammar and of Lambrecht s model are introduced and explicated. The information structure analysis is presented in three chapters, each treating one of the three sentence types. The analyses are based on spoken language data and elicitation. Prosody is included in the study when a syntactic structure seems to code two different focus structures. In such cases, it is pertinent to investigate whether these are coded by prosody. The final chapter presents the constructions that have been established and the problems encountered in analysing them. It also discusses the impact of the study on the theories used and on the theory of syntax in general.

Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA-binding, helical distortion and cleavage, compared to a canonical LAGLIDADG homing endonuclease

Mycobacterium leprae, which has undergone reductive evolution leaving behind a minimal set of essential genes, has retained intervening sequences in four of its genes implicating a vital role for them in the survival of the leprosy bacillus. A single in-frame intervening sequence has been found embedded within its recA gene. Comparison of M. leprae recA intervening sequence with the known intervening sequences indicated that it has the consensus amino acid sequence necessary for being a LAGLIDADG-type homing endonuclease. In light of massive gene decay and function loss in the leprosy bacillus, we sought to investigate whether its recA intervening sequence encodes a catalytically active homing endonuclease. Here we show that the purified M. leprae RecA intein (PI-MleI) binds to cognate DNA and displays endonuclease activity in the presence of alternative divalent cations, Mg2+ or Mn2+. A combination of approaches including four complementary footprinting assays such as DNase I, Cu/phenanthroline, methylation protection and KMnO4, enhancement of 2-aminopurine fluorescence and mapping of the cleavage site revealed that PI-MleI binds to cognate DNA flanking its insertion site, induces helical distortion at the cleavage site and generates two staggered double-strand breaks. Taken together, these results implicate that PI-MleI possess a modular structure with separate domains for DNA target recognition and cleavage, each with distinct sequence preferences. From a biological standpoint, it is tempting to speculate that our findings have implications for understanding the evolution of LAGLIDADG family of homing endonucleases