Screening nucleotide binding to amino acid-coated supports by surface plasmon resonance and nuclear magnetic resonance

Here, we describe a rapid and efficient screening method using surface plasmon resonance (SPR) and saturation transfer difference–nuclear magnetic resonance (STD-NMR) spectroscopy to yield information regarding the residues involved in nucleotide binding to amino acid-coated supports. The aim of this work was to explore the use of these spectroscopic techniques to study amino acid–nucleotide interactions in order to improve the binding specificity of the amino acid ligands used to purify plasmid DNA. For SPR, we present a strategy that immobilizes arginine and lysine on a surface as model supports, and we analyze binding responses when synthetic homo-deoxyoligonucleotides are injected over the amino acid surface. The binding responses are detectable and reproducible despite the small size of the immobilized amino acids. Using STD-NMR, we performed epitope mapping of homo-deoxyoligonucleotides bound to l-arginine–bisoxyran–Sepharose and l-lysine–Sepharose supports. Polynucleotide binding preferences differed; for example, polyC interacted preferentially through its backbone with the two supports, whereas polyT bound the supports through its thymine moiety. STD-NMR combined with SPR measurements was successfully used to screen amino acid–nucleotide interactions and determine the binding affinities of the complexes.     

Analysis of natural red dyes (cochineal) in textiles of historical importance using HPLC and multivariate data analysis

A new analytical approach based on high-performance liquid chromatography with diode array detector (HPLC-DAD) and multivariate data analysis was applied and assessed for analyzing the red dye extracted from cochineal insects, used in precious historical textiles. The most widely used method of analysis involves quantification of specific minor compounds (markers), using HPLC-DAD. However, variation in the cochineal markers concentration, use of aggressive dye extraction methods and poor resolution of HPLC chromatograms can compromise the identification of the precise insect species used in the textiles. In this study, a soft extraction method combined with a new dye recovery treatment was developed, capable of yielding HPLC chromatograms with good resolution, for the first time, for historical cochineal-dyed textiles. After principal components analysis (PCA) and mass spectrometry (MS), it was possible to identify the cochineal species used in these textiles, in contrast to the accepted method of analysis. In order to compare both methodologies, 7 cochineal species and 63 historical cochineal insect specimens were analyzed using the two approaches, and then compared with the results for 15 historical textiles in order to assess their applicability to real complex samples. The methodology developed here was shown to provide more accurate and consistent information than the traditional method. Almost all of the historical textiles were dyed with Porphyrophora sp. insects. These results emphasize the importance of adopting the proposed methodology for future research on cochineal (and related red dyes). Mild extraction methods and HPLC-DAD/MSⁿ analysis yield distinctive profiles, which, in combination with a PCA reference database, are a powerful tool for identifying red insect dyes.     

Vanishing viscosity with short wave-long wave interactions for multi-D scalar conservation laws

We consider a system coupling a multidimensional semilinear Schrödinger equation and a multidimensional nonlinear scalar conservation law with viscosity, which is motivated by a model of short wave-long wave interaction introduced by Benney (1977). We prove the global existence and uniqueness of the solution of the Cauchy problem for this system. We also prove the convergence of the whole sequence of solutions when the viscosity ε and the interaction parameter α approach zero so that α=o(ε1/2). We also indicate how to extend these results to more general systems which couple multidimensional semilinear systems of Schrödinger equations with multidimensional nonlinear systems of scalar conservation laws mildly coupled.     

Energy decay rates of elastic waves in unbounded domain with potential type of damping

In this paper we first show that the total energy of solutions for a semilinear system of elastic waves in Rn with a potential type of damping decays in an algebraic rate to zero. We study the critical potential case and we assume that the initial data have a compact support. An application for the Euler-Poisson-Darboux type dissipation V(t,x) is obtained and in this case the compactness of the support on the initial data is not necessary. Finally, we shall discuss the energy concentration region for the linear system of elastic waves in an exterior domain.     

On the coset laws for skew lattices

Skew lattices are a noncommutative generalization of lattices. In the paper we study the varieties of symmetric, strongly symmetric and cancellative skew lattices, and characterize them in terms of certain laws regarding the coset structure of a skew lattice. As a consequence, combinatorial results connecting powers of D{\mathcal{D}}-classes and indices are derived.     

Incompressible surfaces in handlebodies and boundary reducible 3-manifolds

We study the existence of incompressible embeddings of surfaces into the genus two handlebody. We show that for every compact surface with boundary, orientable or not, there is an incompressible embedding of the surface into the genus two handlebody. In the orientable case the embedding can be either separating or non-separating. We also consider the case in which the genus two handlebody is replaced by an orientable 3-manifold with a compressible boundary component of genus greater than or equal to two.     

Weak Solutions for the Motion of a Self-propelled Deformable Structure in a Viscous Incompressible Fluid

We consider the three-dimensional motion of a self-propelled deformable structure into a viscous incompressible fluid. The deformation of the solid is given whereas its position is unknown. Such a system could model the propulsion of fish-like swimmers. The equations of motion of the fluid are the Navier-Stokes equations and the equations for the structure are deduced from Newton’s laws. The corresponding system is a free boundary problem and the main result of the paper is the existence of weak solutions for this problem.     

Evaluación de la habitabilidad de edificios afectados por sismo utilizando la teoría de conjuntos difusos y las redes neuronales artificiales

The fuzzy sets theory and the artificial neural networks are computational intelligence tools which are nowadays widely used in earthquake engineering. This paper develops a method and a computer program which use these computational intelligence tools in order to support the damage and safety evaluation of buildings after strong earthquakes. The model uses an artificial neural network with three layers and a Kohonen learning algorithm; it also uses fuzzy sets in order to manage subjective information such as linguistic qualification of the damage levels in buildings and a fuzzy rule base to support the decision making process. All these techniques are incorporated in the developed computer program. The input data is the subjective and incomplete information about the building state obtained by possibly non experienced evaluators in the field of the seismic performance of buildings. The proposed method is implemented in a tool especially useful in the emergency response phase, when it supports the decision making regarding the building habitability and reparability. In order to show its effectiveness, two examples are included for two different types of buildings.     

The constrained compartmentalized knapsack problem: mathematical models and solution methods

The constrained compartmentalized knapsack problem can be seen as an extension of the constrained knapsack problem. However, the items are grouped into different classes so that the overall knapsack has to be divided into compartments, and each compartment is loaded with items from the same class. Moreover, building a compartment incurs a fixed cost and a fixed loss of the capacity in the original knapsack, and the compartments are lower and upper bounded. The objective is to maximize the total value of the items loaded in the overall knapsack minus the cost of the compartments. This problem has been formulated as an integer non-linear program, and in this paper, we reformulate the non-linear model as an integer linear master problem with a large number of variables. Some heuristics based on the solution of the restricted master problem are investigated. A new and more compact integer linear model is also presented, which can be solved by a branch-and-bound commercial solver that found most of the optimal solutions for the constrained compartmentalized knapsack problem. On the other hand, heuristics provide good solutions with low computational effort.