Symmetry in biology: from genetic code to stochastic gene regulation

Mathematical models, as instruments for understanding the workings of nature, are a traditional tool of physics, but they also play an ever increasing role in biology - in the description of fundamental processes as well as that of complex systems. In this review, the authors discuss two examples of the application of group theoretical methods, which constitute the mathematical discipline for a quantitative description of the idea of symmetry, to genetics. The first one appears, in the form of a pseudo-orthogonal (Lorentz like) symmetry, in the stochastic modelling of what may be regarded as the simplest possible example of a genetic network and, hopefully, a building block for more complicated ones: a single self-interacting or externally regulated gene with only two possible states: ` on` and ` off`. The second is the algebraic approach to the evolution of the genetic code, according to which the current code results from a dynamical symmetry breaking process, starting out from an initial state of complete symmetry and ending in the presently observed final state of low symmetry. In both cases, symmetry plays a decisive role: in the first, it is a characteristic feature of the dynamics of the gene switch and its decay to equilibrium, whereas in the second, it provides the guidelines for the evolution of the coding rules.

Skew-symmetric identities of octonions

Quadratic alternative superalgebras are introduced and their super-identities and central functions on one odd generator are described. As a corollary, all multilinear skew-symmetric identities and central polynomials of octonions are classified. (C) 2008 Elsevier B.V. All rights reserved.

A stronger Dunford-Pettis property

We discuss a strong version of the Dunford-Pettis property, earlier named (DP*) property, which is shared by both l(1) and l(infinity) It is equivalent to the Dunford-Pettis property plus the fact that every quotient map onto c(0) is completely continuous. Other weak sequential continuity results on polynomials and analytic mappings related to the (DP*) property are shown.

Finite-dimensional non-associative algebras and codimension growth

Let A be a (non-necessarily associative) finite-dimensional algebra over a field of characteristic zero. A quantitative estimate of the polynomial identities satisfied by A is achieved through the study of the asymptotics of the sequence of codimensions of A. It is well known that for such an algebra this sequence is exponentially bounded. Here we capture the exponential rate of growth of the sequence of codimensions for several classes of algebras including simple algebras with a special non-degenerate form, finite-dimensional Jordan or alternative algebras and many more. In all cases such rate of growth is integer and is explicitly related to the dimension of a subalgebra of A. One of the main tools of independent interest is the construction in the free non-associative algebra of multialternating polynomials satisfying special properties. (C) 2010 Elsevier Inc. All rights reserved.

A full family of multimodal maps on the circle

We exhibit a family of trigonometric polynomials inducing a family of 2m-multimodal maps on the circle which contains all relevant dynamical behavior.

Maslov index in semi-Riemannian submersions

We study focal points and Maslov index of a horizontal geodesic gamma : I -> M in the total space of a semi-Riemannian submersion pi : M -> B by determining an explicit relation with the corresponding objects along the projected geodesic pi omicron gamma : I -> B in the base space. We use this result to calculate the focal Maslov index of a (spacelike) geodesic in a stationary spacetime which is orthogonal to a timelike Killing vector field.

Pseudo Focal Points Along Lorentzian Geodesics and Morse Index

Given a Lorentzian manifold (M,g), a geodesic gamma in M and a timelike Jacobi field Y along gamma, we introduce a special class of instants along gamma that we call Y-pseudo conjugate (or focal relatively to some initial orthogonal submanifold). We prove that the Y-pseudo conjugate instants form a finite set, and their number equals the Morse index of (a suitable restriction of) the index form. This gives a Riemannian-like Morse index theorem. As special cases of the theory, we will consider geodesics in stationary and static Lorentzian manifolds, where the Jacobi field Y is obtained as the restriction of a globally defined timelike Killing vector field.

UNIFORM APPROXIMATION ON IDEALS OF MULTILINEAR MAPPINGS

For each ideal of multilinear mappings M we explicitly construct a corresponding ideal (a)M such that multilinear forms in (a)M are exactly those which can be approximated, in the uniform norm, by multilinear forms in M. This construction is then applied to finite type, compact, weakly compact and absolutely summing multilinear mappings. It is also proved that the correspondence M bar right arrow (a)M. IS Aron-Berner stability preserving.

Contravariantly finite subcategories closed under predecessors

Let A be an Artin algebra and mod A be the category of finitely generated right A-modules. We prove that an additive full subcategory C of mod A closed under predecessors is contravariantly finite if and only if its right Ext-orthogonal is covariantly finite, or if and only if the Ext-injectives in C define a cotilting module (over the support algebra of C) or, equivalently, if and only if C is the support of the representable functors given by the Ext-injectives. (C) 2009 Elsevier Inc. All rights reserved.

Thermo-solvatochromism of merocyanine polarity probes - What are the consequences of increasing probe lipophilicity through annelation?

The question raised in the title has been answered by comparing the solvatochromism of two series of polarity probes, the lipophilicities of which were increased either by increasing the length of an alkyl group (R) attached to a fixed pyridine-based structure or through annelation (i.e., by fusing benzene rings onto a central pyridine-based structure). The following novel solvatochromic probes were synthesized: 2,6-dibromo-4-[(E)-2-(1-methylquinolinium-4-yl)ethenyl]-phenolate (MeQMBr(2)) and 2,6-dibromo-4-[(E)-2-(1-methyl-acridinium-4- yl) ethenyl)]phenolate (MeAMBr(2) The solvatochromic behavior of these probes, along with that of 2,6dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl]phenol-ate(MePMBr(2)) was analyzed in terms of increasing probe lipophilicity, through annelation. Values of the empirical solvent polarity scale [E(T)(MePMBr(2))] in kcalmol(-1) correlated linearly with ET(30), the corresponding values for the extensively employed probe 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl)phenolate (RB). On the other hand, the nonlinear correlations of ET(MeQMBr(2)) or ET(MeAMBr(2)) with E(T)(30) are described by second-order polynomials. Possible reasons for this behavior include: i) self-aggregation of the probe, ii) photoinduced cis/trans isomerization of the dye, and iii) probe structure- and solvent-dependent contributions of the quinonoid and zwitterionic limiting formulas to the ground and excited states of the probe. We show that mechanisms (i) and (ii) are not operative under the experimental conditions employed; experimental evidence (NMR) and theoretical calculations are presented to support the conjecture that the length of the central ethenylic bond in the dye increases in the order MeAMBr(2) > MeQMBr(2) > MePMBr(2), That is, the contribution of the zwitterionic limiting formula predominates for the latter probe, as is also the case for RB, this being the reason for the observed linear correlation between the ET(MePMBr2) and the ET(30) scales. The effect of increasing probe lipophilicity on solvatochromic behavior therefore depends on the strategy employed. Increasing the length of R affects solvatochromism much less than annelation, because the former structural change hardly perturbs the energy of the intramolecular charge-transfer transition responsible for solvatochromism. The thermo-solvatochromic behavior (effect of temperature on solvatochromism) of the three probes was studied in mixtures of water with propanol and/or with DMSO. The solvation model used explicitly considers the presence of three ""species"" in the system: bulk solution and probe solvation shell [namely, water (W), organic solvent (Solv)], and solvent-water hydrogen-bonded aggregate (Solv-W). For aqueous propanol, the probe is efficiently solvated by Solv-W; the strong interaction of DMSO with W drastically decreases the efficiency of Solv-W in solvating the probe, relative to its precursor solvents. Temperature increases resulted in desolvation of the probes, due to the concomitant reduction in the structured characters of the components of the binary mixtures.

Traffic and Road Sign Recognition

This thesis presents a system to recognise and classify road and traffic signs for the purpose of developing an inventory of them which could assist the highway engineers’ tasks of updating and maintaining them. It uses images taken by a camera from a moving vehicle. The system is based on three major stages: colour segmentation, recognition, and classification. Four colour segmentation algorithms are developed and tested. They are a shadow and highlight invariant, a dynamic threshold, a modification of de la Escalera’s algorithm and a Fuzzy colour segmentation algorithm. All algorithms are tested using hundreds of images and the shadow-highlight invariant algorithm is eventually chosen as the best performer. This is because it is immune to shadows and highlights. It is also robust as it was tested in different lighting conditions, weather conditions, and times of the day. Approximately 97% successful segmentation rate was achieved using this algorithm.Recognition of traffic signs is carried out using a fuzzy shape recogniser. Based on four shape measures - the rectangularity, triangularity, ellipticity, and octagonality, fuzzy rules were developed to determine the shape of the sign. Among these shape measures octangonality has been introduced in this research. The final decision of the recogniser is based on the combination of both the colour and shape of the sign. The recogniser was tested in a variety of testing conditions giving an overall performance of approximately 88%.Classification was undertaken using a Support Vector Machine (SVM) classifier. The classification is carried out in two stages: rim’s shape classification followed by the classification of interior of the sign. The classifier was trained and tested using binary images in addition to five different types of moments which are Geometric moments, Zernike moments, Legendre moments, Orthogonal Fourier-Mellin Moments, and Binary Haar features. The performance of the SVM was tested using different features, kernels, SVM types, SVM parameters, and moment’s orders. The average classification rate achieved is about 97%. Binary images show the best testing results followed by Legendre moments. Linear kernel gives the best testing results followed by RBF. C-SVM shows very good performance, but ?-SVM gives better results in some case.

Reservoir Management For Flood And Drought Protection Using Infinite Horizon Model Predictive Control

Model Predictive Control (MPC) is a control method that solves in real time an optimal control problem over a finite horizon. The finiteness of the horizon is both the reason of MPC's success and its main limitation. In operational water resources management, MPC has been in fact successfully employed for controlling systems with a relatively short memory, such as canals, where the horizon length is not an issue. For reservoirs, which have generally a longer memory, MPC applications are presently limited to short term management only. Short term reservoir management can be effectively used to deal with fast process, such as floods, but it is not capable of looking sufficiently ahead to handle long term issues, such as drought. To overcome this limitation, we propose an Infinite Horizon MPC (IH-MPC) solution that is particularly suitable for reservoir management. We propose to structure the input signal by use of orthogonal basis functions, therefore reducing the optimization argument to a finite number of variables, and making the control problem solvable in a reasonable time. We applied this solution for the management of the Manantali Reservoir. Manantali is a yearly reservoir located in Mali, on the Senegal river, affecting water systems of Mali, Senegal, and Mauritania. The long term horizon offered by IH-MPC is necessary to deal with the strongly seasonal climate of the region.

Análise dinâmica de solos submetidos à ação simultânea das três componentes da excitação na base rochosa

Durante a análise sísmica de estruturas complexas, o modelo matemático empregado deveria incluir não só as distribuicões irregulares de massas e de rigidezes senão também à natureza tridimensional da ecitação sísmica. Na prática, o elevado número de graus de liberdade involucrado limita este tipo de análise à disponibilidade de grandes computadoras. Este trabalho apresenta um procedimento simplificado, para avaliar a amplificação do movimento sísmico em camadas de solos. Sua aplicação permitiria estabelecer critérios a partir dos quais avalia-se a necessidade de utilizar modelos de interação solo-estrutura mais complexos que os utilizados habitualmente. O procedimento proposto possui as seguientes características : A- Movimento rígido da rocha definido em termos de três componentes ortagonais. Direção de propagação vertical. B- A ecuação constitutiva do solo inclui as características de não linearidade, plasticidade, dependência da história da carga, dissipação de energia e variação de volume. C- O perfil de solos é dicretizado mediante um sistema de massas concentradas. Utiliza-se uma formulação incremental das equações de movimento com integração directa no domínio do tempo. As propriedades pseudo-elásticas do solo são avaliadas em cada intervalo de integração, em função do estado de tensões resultante da acção simultânea das três componentes da excitação. O correcto funcionamento do procedimento proposto é verificado mediante análises unidimensionais (excitação horizontal) incluindo estudos comparativos com as soluções apresentadas por diversos autores. Similarmente apresentam-se análises tridimensionais (acção simultânea das três componentes da excitação considerando registros sísmicos reais. Analisa-se a influência que possui a dimensão da análise (uma análise tridimensional frente a três análises unidimensionais) na resposta de camadas de solos submetidos a diferentes níveis de exçitação; isto é, a limitação do Princípio de Superposisão de Efeitos.

A metodologia de análise de dados espaciais aplicada a plantas forrageiras

Dois experimentos e um levantamento por amostragem foram analisados no contexto de dados espaciais. Os experimentos foram delineados em blocos completos casualizados sendo que no experimento um (EXP 1) foram avaliados oito cultivares de trevo branco, sendo estudadas as variáveis Matéria Seca Total (MST) e Matéria Seca de Gramíneas (MSGRAM) e no experimento dois (EXP 2) 20 cultivares de espécies forrageiras, onde foi estudada a variável Percentagem de Implantação (%IMPL). As variáveis foram analisadas no contexto de modelos mistos, sendo modelada a variabilidade espacial através de semivariogramas exponencias, esféricos e gaussianos. Verificou-se uma diminuição em média de 19% e 14% do Coeficiente de Variação (CV) das medias dos cultivares, e uma diminuição em média de 24,6% e 33,3% nos erros padrões dos contrastes ortogonais propostos em MST e MSGRAM. No levantamento por amostragem, estudou-se a associação espacial em Aristida laevis (Nees) Kunth , Paspalum notatum Fl e Demodium incanum DC, amostrados em uma transecção fixa de quadros contiguos, a quatro tamanhos de unidades amostrais (0,1x0,1m; 0,1x0,3m; 0,1x0,5m; e 0,1x1,0m). Nas espécies Aristida laevis (Nees) Kunth e Paspalum notatum Fl, existiu um bom ajuste dos semivariogramas a tamanhos menores das unidades amostrais, diminuíndo quando a unidade amostral foi maior. Desmodium incanum DC apresentou comportamento contrario, ajustando melhor os semivariogramas a tamanhos maiores das unidades amostrais.

A Common-feature approach for testing present-value restrictions with financial data

It is well known that cointegration between the level of two variables (labeled Yt and yt in this paper) is a necessary condition to assess the empirical validity of a present-value model (PV and PVM, respectively, hereafter) linking them. The work on cointegration has been so prevalent that it is often overlooked that another necessary condition for the PVM to hold is that the forecast error entailed by the model is orthogonal to the past. The basis of this result is the use of rational expectations in forecasting future values of variables in the PVM. If this condition fails, the present-value equation will not be valid, since it will contain an additional term capturing the (non-zero) conditional expected value of future error terms. Our article has a few novel contributions, but two stand out. First, in testing for PVMs, we advise to split the restrictions implied by PV relationships into orthogonality conditions (or reduced rank restrictions) before additional tests on the value of parameters. We show that PV relationships entail a weak-form common feature relationship as in Hecq, Palm, and Urbain (2006) and in Athanasopoulos, Guillén, Issler and Vahid (2011) and also a polynomial serial-correlation common feature relationship as in Cubadda and Hecq (2001), which represent restrictions on dynamic models which allow several tests for the existence of PV relationships to be used. Because these relationships occur mostly with nancial data, we propose tests based on generalized method of moment (GMM) estimates, where it is straightforward to propose robust tests in the presence of heteroskedasticity. We also propose a robust Wald test developed to investigate the presence of reduced rank models. Their performance is evaluated in a Monte-Carlo exercise. Second, in the context of asset pricing, we propose applying a permanent-transitory (PT) decomposition based on Beveridge and Nelson (1981), which focus on extracting the long-run component of asset prices, a key concept in modern nancial theory as discussed in Alvarez and Jermann (2005), Hansen and Scheinkman (2009), and Nieuwerburgh, Lustig, Verdelhan (2010). Here again we can exploit the results developed in the common cycle literature to easily extract permament and transitory components under both long and also short-run restrictions. The techniques discussed herein are applied to long span annual data on long- and short-term interest rates and on price and dividend for the U.S. economy. In both applications we do not reject the existence of a common cyclical feature vector linking these two series. Extracting the long-run component shows the usefulness of our approach and highlights the presence of asset-pricing bubbles.