alpha-Helices are peculiar atomic arrangements characterizing protein structures. Their occurrence can be used within crystallographic methods as minimal a priori information to drive the phasing process towards solution. Recently, brute-force methods have been developed which search for all possible positions of alpha-helices in the crystal cell by molecular replacement and explore all of them systematically. Knowing the alpha-helix orientations in advance would be a great advantage for this kind of approach. For this purpose, a fully automatic procedure to find alpha-helix orientations within the Patterson map has been developed. The method is based on Fourier techniques specifically addressed to the identification of helical shapes and operating on Patterson maps described in spherical coordinates. It supplies a list of candidate orientations, which are then refined by using a figure of merit based on a rotation function calculated for a template polyalanine helix oriented along the current direction. The orientation search algorithm has been optimized to work at 3 A resolution, while the candidates are refined against all measured reflections. The procedure has been applied to a large number of protein test structures, showing an overall efficiency of 77% in finding alpha-helix orientations, which decreases to 48% on limiting the number of candidate solutions (to 13 on average). The information obtained may be used in many aspects in the framework of molecular-replacement phasing, as well as to constrain the generation of models in computational modelling programs. The procedure will be accessible through the next release of IL MILIONE and could be decisive in the solution of new unknown structures.

Per circa un millennio, l'ambra ha goduto di una particolare fortuna in Puglia e nella vicina Basilicata, tanto da costituire uno dei principali fossili-guida utilizzati per ricostruire la storia archeologica della regione. Particolarmente interessante è la diffusione delle ambre figurate nel Basso Adriatico, presenti esclusivamente nelle ricche sepolture indigene della Puglia centro-settentrionale (Peucezia e Daunia) durante la fase preromana, con la pressochè totale esclusione del distretto meridionale (Messapia) e con qualche sporadica testimonianza a Taranto. Il volume rappresenta un primo importante tentativo verso una classificazione tipologica delle ambre figurate rinvenute nella Puglia preromana, in un arco cronologico che va dal VII al IV secolo a.C.

We present a one space dimensional model with finite speed of propagation for population dynamics, based both on the hyperbolic Cattaneo dynamics and the evolutionary game theory. We prove analytical properties of the model and global estimates for solutions, by using a hyperbolic nonlinear Trotter product formula.

We introduce a new class of finite difference schemes for approximating the solutions to an initial-boundary value problem on a bounded interval for a one-dimensional dissipative hyperbolic system with an external source term, which arises as a simple model of chemotaxis. Since the solutions to this problem may converge to nonconstant asymptotic states for large times, standard schemes usually fail to yield a good approximation. Therefore, we propose a new class of schemes, which use an asymptotic higher order correction, second and third order in our examples, to balance the effects of the source term and the influence of the asymptotic solutions. Special care is needed to deal with boundary conditions to avoid harmful loss of mass. Convergence results are proved for these new schemes, and several numerical tests are presented and discussed to verify the effectiveness of their behavior.

In this paper, by applying a variation of the backward Euler method, we propose a discrete-time SIR epidemic model whose discretization scheme preserves the global asymptotic stability of equilibria for a class of corresponding continuous-time SIR epidemic models. Using discrete-time analogue of Lyapunov functionals, the global asymptotic stability of the equilibria is fully determined by the basic reproduction number, when the infection incidence rate has a suitable monotone property.

In this paper, by constructing Lyapunov functionals, we consider the global dynamics of an SIRS epidemic model with a wide class of nonlinear incidence rates and distributed delays h 0 p(? )f (S(t), I (t - ?))d? under the condition that the total population converges to 1. By using a technical lemma which is derived from strong condition of strict monotonicity of functions f (S,I) and f (S,I)/I with respect to S >= 0 and I > 0, we extend the global stability result for an SIR epidemic model

Inflammation is part of a complex physiological response to harmful stimuli and pathogenic stress. The five components of the Nuclear Factor ?B (NF-?B) family are prominent mediators of inflammation, acting as key transcriptional regulators of hundreds of genes. Several signaling pathways activated by diverse stimuli converge on NF-?B activation, resulting in a regulatory system characterized by high complexity. It is increasingly recognized that the number of components that impinges upon phenotypic outcomes of signal transduction pathways may be higher than those taken into consideration from canonical pathway representations. Scope of the present analysis is to provide a wider, systemic picture of the NF-?B signaling system. Data from different sources such as literature, functional enrichment web resources, protein-protein interaction and pathway databases have been gathered, curated, integrated and analyzed in order to reconstruct a single, comprehensive picture of the proteins that interact with, and participate to the NF-?B activation system. Such a reconstruction shows that the NF-?B interactome is substantially different in quantity and quality of components with respect to canonical representations. The analysis highlights that several neglected but topologically central proteins may play a role in the activation of NF-?B mediated responses. Moreover the interactome structure fits with the characteristics of a bow tie architecture. This interactome is intended as an open network resource available for further development, refinement and analysis.

Spatially explicit models consisting of reaction-diffusion partial differential equations are considered in order to model prey-predator interactions, since it is known that the role of spatial processes reveals of great interest in the study of the effects of habitat fragmentation on biodiversity. As almost all of the realistic models in biology, these models are nonlinear and their solution is not knwon is closed form. Our aim is approximating the solution itself by means of exponential Runge-Kutta integrators. Moreover, we apply the shift-and-invert Krylov approach in order to evaluate the entire functions needed for implementing the exponential method. This numerical procedure reveals to be very efficient in avoiding numerical instability during the simulation, since it allows us to adopt high order in the accuracy.