Kinetics of self-assembling microtubules: an "inverse problem" in biochemistry.

Experimental time series for a nonequilibrium reaction may in some cases contain sufficient data to determine a unique kinetic model for the reaction by a systematic mathematical analysis. As an example, a kinetic model for the self-assembly of microtubules is derived here from turbidity time series for solutions in which microtubules assemble. The model may be seen as a generalization of Oosawa's classical nucleation-polymerization model. It reproduces the experimental data with a four-stage nucleation process and a critical nucleus of 15 monomers.

Calculating the probability of multitaxon evolutionary trees: bootstrappers Gambit.

The reconstruction of multitaxon trees from molecular sequences is confounded by the variety of algorithms and criteria used to evaluate trees, making it difficult to compare the results of different analyses. A global method of multitaxon phylogenetic reconstruction described here, Bootstrappers Gambit, can be used with any four-taxon algorithm, including distance, maximum likelihood, and parsimony methods. It incorporates a Bayesian-Jeffreys'-bootstrap analysis to provide a uniform probability-based criterion for comparing the results from diverse algorithms. To examine the usefulness of the method, the origin of the eukaryotes has been investigated by the analysis of ribosomal small subunit RNA sequences. Three common algorithms (paralinear distances, Jukes-Cantor distances, and Kimura distances) support the eocyte topology, whereas one (maximum parsimony) supports the archaebacterial topology, suggesting that the eocyte prokaryotes are the closest prokaryotic relatives of the eukaryotes.

Decreased atherosclerosis in mice deficient in both macrophage colony-stimulating factor (op) and apolipoprotein E.

To develop a murine model system to test the role of monocyte-derived macrophage in atherosclerosis, the osteopetrotic (op) mutation in the macrophage colony-stimulating factor gene was bred onto the apolipoprotein E (apoE)-deficient background. The doubly mutant (op/apoE-deficient) mice fed a low-fat chow diet had significantly smaller proximal aortic lesions at an earlier stage of progression than their apoE-deficient control littermates. These lesions in the doubly mutant mice were composed of macrophage foam cells. The op/apoE-deficient mice also had decreased body weights, decreased blood monocyte differentials, and increased mean cholesterol levels of approximately 1300 mg/dl. Statistical analysis determined that atherosclerosis lesion area was significantly affected by the op genotype and gender. The confounding variables of body weight, plasma cholesterol, and monocyte differential, which were all affected by op genotype, had no significant additional effect on lesion area once they were adjusted for the effects of op genotype and gender. Unexpectedly, there was a significant inverse correlation between plasma cholesterol and lesion area, implying that each may be the result of a common effect of macrophage colony-stimulating factor levels. The data support the hypothesis that macrophage colony-stimulating factor and its effects on macrophage development and function play a key role in atherogenesis.

On the existence and implications of an inverse folding code in proteins.

The existence of a code relating the set of possible sequences at a given position in a protein backbone to the local structure at that location is investigated. It is shown that only 73% of 4-C alpha structure fragments in a sample of 114 protein structures exhibit a preference for a particular set of sequences. The remaining structures can accommodate essentially any sequence. The structures that encode specific sequence distributions include the classical "secondary" structures, with the notable exception of planar (beta) bends. It is suggested that this has implications as to the mechanism of folding in proteins with extensive sheet/barrel structure. The possible role of structures that do not encode specific sequences as mutation hot spots is noted.

Enhancers increase the probability but not the level of gene expression.

We have studied enhancer function in transient and stable expression assays in mammalian cells by using systems that distinguish expressing from nonexpressing cells. When expression is studied in this way, enhancers are found to increase the probability of a construct being active but not the level of expression per template. In stably integrated constructs, large differences in expression level are observed but these are not related to the presence of an enhancer. Together with earlier studies, these results suggest that enhancers act to affect a binary (on/off) switch in transcriptional activity. Although this idea challenges the widely accepted model of enhancer activity, it is consistent with much, if not all, experimental evidence on this subject. We hypothesize that enhancers act to increase the probability of forming a stably active template. When randomly integrated into the genome, enhancers may affect a metastable state of repression/activity, permitting expression in regions that would not permit activity of an isolated promoter.

Sampling Quantum Nonlocal Correlations with High Probability

It is well known that quantum correlations for bipartite dichotomic measurements are those of the form (Formula presented.), where the vectors ui and vj are in the unit ball of a real Hilbert space. In this work we study the probability of the nonlocal nature of these correlations as a function of (Formula presented.), where the previous vectors are sampled according to the Haar measure in the unit sphere of (Formula presented.). In particular, we prove the existence of an (Formula presented.) such that if (Formula presented.), (Formula presented.) is nonlocal with probability tending to 1 as (Formula presented.), while for (Formula presented.), (Formula presented.) is local with probability tending to 1 as (Formula presented.).

Three-dimensional inverse modelling of magnetic anomaly sources based on a genetic algorithm.

We present a modelling method to estimate the 3-D geometry and location of homogeneously magnetized sources from magnetic anomaly data. As input information, the procedure needs the parameters defining the magnetization vector (intensity, inclination and declination) and the Earth's magnetic field direction. When these two vectors are expected to be different in direction, we propose to estimate the magnetization direction from the magnetic map. Then, using this information, we apply an inversion approach based on a genetic algorithm which finds the geometry of the sources by seeking the optimum solution from an initial population of models in successive iterations through an evolutionary process. The evolution consists of three genetic operators (selection, crossover and mutation), which act on each generation, and a smoothing operator, which looks for the best fit to the observed data and a solution consisting of plausible compact sources. The method allows the use of non-gridded, non-planar and inaccurate anomaly data and non-regular subsurface partitions. In addition, neither constraints for the depth to the top of the sources nor an initial model are necessary, although previous models can be incorporated into the process. We show the results of a test using two complex synthetic anomalies to demonstrate the efficiency of our inversion method. The application to real data is illustrated with aeromagnetic data of the volcanic island of Gran Canaria (Canary Islands).

Search for signatures of magnetically-induced alignment in the arrival directions measured by the Pierre Auger Observatory

We present the results of an analysis of data recorded at the Pierre Auger Observatory in which we search for groups of directionally-aligned events (or 'multiplets') which exhibit a correlation between arrival direction and the inverse of the energy. These signatures are expected from sets of events coming from the same source after having been deflected by intervening coherent magnetic fields. The observation of several events from the same source would open the possibility to accurately reconstruct the position of the source and also measure the integral of the component of the magnetic field orthogonal to the trajectory of the cosmic rays. We describe the largest multiplets found and compute the probability that they appeared by chance from an isotropic distribution. We find no statistically significant evidence for the presence of multiplets arising from magnetic deflections in the present data. (C) 2011 Elsevier B.V. All rights reserved.

Reconciliação de dados de uma malha de gasodutos.

O trabalho aborda a aplicação da técnica de reconciliação de dados para o balanço da movimentação de gás natural em uma malha de escoamento de gás não processado, elaborando também um método de cálculo rápido de inventário de um duto. Foram aplicadas, separadamente, a reconciliação volumétrica à condição padrão de medição e a reconciliação mássica, bem como realizadas comparações dos resultados em relação ao balanço original e verificação do balanço resultante de energia em termos de poder calorífico superior. Dois conjuntos de pesos foram aplicados, um arbitrado de acordo com o conhecimento prévio da qualidade do sistema de medição de cada um dos pontos, outro baseado no inverso da variância dos volumes diários apurados no período. Ambos apresentaram bons resultados e o segundo foi considerado o mais apropriado. Por meio de uma abordagem termodinâmica, foi avaliado o potencial impacto, ao balanço, da condensação de parte da fase gás ao longo do escoamento e a injeção de um condensado de gás natural não estabilizado por uma das fontes. Ambos tendem a impactar o balanço, sendo o resultado esperado um menor volume, massa e energia de fase gás na saída. Outros fatores de considerável impacto na qualidade dos dados e no resultado final da reconciliação são a qualidade da medição de saída do sistema e a representatividade da composição do gás neste ponto. O inventário é calculado a partir de uma regressão que se baseia em um regime permanente de escoamento, o que pode apresentar maior desvio quando fortes transientes estão ocorrendo no último dia do mês, porém a variação de inventário ao longo do mês possui baixo impacto no balanço. Concluiu-se que a reconciliação volumétrica é a mais apropriada para este sistema, pois os dados reconciliados levam os balanços mássicos e de energia em termos de poder calorífico, ambos na fase gás, para dentro do perfil esperado de comportamento. Embora um balanço volumétrico nulo apenas da fase gás não seja por si só o comportamento esperado quando se considera os efeitos descritos, para desenvolver um balanço mais robusto é necessário considerar as frações líquidas presentes no sistema, agregando maior dificuldade na aquisição e qualidade dos dados.

The Lateral Trigger Probability function for the Ultra-High Energy Cosmic Ray showers detected by the Pierre Auger Observatory

In this paper we introduce the concept of Lateral Trigger Probability (LTP) function, i.e., the probability for an Extensive Air Shower (EAS) to trigger an individual detector of a ground based array as a function of distance to the shower axis, taking into account energy, mass and direction of the primary cosmic ray. We apply this concept to the surface array of the Pierre Auger Observatory consisting of a 1.5 km spaced grid of about 1600 water Cherenkov stations. Using Monte Carlo simulations of ultra-high energy showers the LTP functions are derived for energies in the range between 10(17) and 10(19) eV and zenith angles up to 65 degrees. A parametrization combining a step function with an exponential is found to reproduce them very well in the considered range of energies and zenith angles. The LTP functions can also be obtained from data using events simultaneously observed by the fluorescence and the surface detector of the Pierre Auger Observatory (hybrid events). We validate the Monte Carlo results showing how LTP functions from data are in good agreement with simulations.

An inverse method to obtain porosity, fibre diameter and density of fibrous sound absorbing materials

Characterization of sound absorbing materials is essential to predict its acoustic behaviour. The most commonly used models to do so consider the flow resistivity, porosity, and average fibre diameter as parameters to determine the acoustic impedance and sound absorbing coefficient. Besides direct experimental techniques, numerical approaches appear to be an alternative to estimate the material’s parameters. In this work an inverse numerical method to obtain some parameters of a fibrous material is presented. Using measurements of the normal incidence sound absorption coefficient and then using the model proposed by Voronina, subsequent application of basic minimization techniques allows one to obtain the porosity, average fibre diameter and density of a sound absorbing material. The numerical results agree fairly well with the experimental data.

Use of an Inverse Method for Time Series to Estimate the Dynamics of and Management Strategies for the Box Jellyfish Carybdea marsupialis

Frequently, population ecology of marine organisms uses a descriptive approach in which their sizes and densities are plotted over time. This approach has limited usefulness for design strategies in management or modelling different scenarios. Population projection matrix models are among the most widely used tools in ecology. Unfortunately, for the majority of pelagic marine organisms, it is difficult to mark individuals and follow them over time to determine their vital rates and built a population projection matrix model. Nevertheless, it is possible to get time-series data to calculate size structure and densities of each size, in order to determine the matrix parameters. This approach is known as a “demographic inverse problem” and it is based on quadratic programming methods, but it has rarely been used on aquatic organisms. We used unpublished field data of a population of cubomedusae Carybdea marsupialis to construct a population projection matrix model and compare two different management strategies to lower population to values before year 2008 when there was no significant interaction with bathers. Those strategies were by direct removal of medusae and by reducing prey. Our results showed that removal of jellyfish from all size classes was more effective than removing only juveniles or adults. When reducing prey, the highest efficiency to lower the C. marsupialis population occurred when prey depletion affected prey of all medusae sizes. Our model fit well with the field data and may serve to design an efficient management strategy or build hypothetical scenarios such as removal of individuals or reducing prey. TThis This sdfsdshis method is applicable to other marine or terrestrial species, for which density and population structure over time are available.

An adaptive algorithm for clustering cumulative probability distribution functions using the Kolmogorov–Smirnov two-sample test

This paper proposes an adaptive algorithm for clustering cumulative probability distribution functions (c.p.d.f.) of a continuous random variable, observed in different populations, into the minimum homogeneous clusters, making no parametric assumptions about the c.p.d.f.’s. The distance function for clustering c.p.d.f.’s that is proposed is based on the Kolmogorov–Smirnov two sample statistic. This test is able to detect differences in position, dispersion or shape of the c.p.d.f.’s. In our context, this statistic allows us to cluster the recorded data with a homogeneity criterion based on the whole distribution of each data set, and to decide whether it is necessary to add more clusters or not. In this sense, the proposed algorithm is adaptive as it automatically increases the number of clusters only as necessary; therefore, there is no need to fix in advance the number of clusters. The output of the algorithm are the common c.p.d.f. of all observed data in the cluster (the centroid) and, for each cluster, the Kolmogorov–Smirnov statistic between the centroid and the most distant c.p.d.f. The proposed algorithm has been used for a large data set of solar global irradiation spectra distributions. The results obtained enable to reduce all the information of more than 270,000 c.p.d.f.’s in only 6 different clusters that correspond to 6 different c.p.d.f.’s.