The crystal structure of the leptospiral hypothetical protein LIC12922 reveals homology with the periplasmic chaperone SurA

Leptospirosis is a world spread zoonosis caused by members of the genus Leptospira. Although leptospires were identified as the causal agent of leptospirosis almost 100 years ago, little is known about their biology, which hinders the development of new treatment and prevention strategies. One of the several aspects of the leptospiral biology not yet elucidated is the process by which outer membrane proteins (OMPs) traverse the periplasm and are inserted into the outer membrane. The crystal structure determination of the conserved hypothetical protein LIC12922 from Leptospira interrogans revealed a two domain protein homologous to the Escherichia coli periplasmic chaperone SurA. The LIC12922 NC-domain is structurally related to the chaperone modules of E. coli SurA and trigger factor, whereas the parvulin domain is devoid of peptidyl prolyl cis-trans isomerase activity. Phylogenetic analyses suggest a relationship between LIC12922 and the chaperones PrsA, PpiD and SurA. Based on our structural and evolutionary analyses, we postulate that LIC12922 is a periplasmic chaperone involved in OMPs biogenesis in Leptospira spp. Since LIC12922 homologs were identified in all spirochetal genomes sequenced to date, this assumption may have implications for the OMPs biogenesis studies not only in leptospires but in the entire Phylum Spirochaetes. (C) 2010 Elsevier Inc. All rights reserved.

Selecting salient objects in real scenes: An oscillatory correlation model

Attention is a critical mechanism for visual scene analysis. By means of attention, it is possible to break down the analysis of a complex scene to the analysis of its parts through a selection process. Empirical studies demonstrate that attentional selection is conducted on visual objects as a whole. We present a neurocomputational model of object-based selection in the framework of oscillatory correlation. By segmenting an input scene and integrating the segments with their conspicuity obtained from a saliency map, the model selects salient objects rather than salient locations. The proposed system is composed of three modules: a saliency map providing saliency values of image locations, image segmentation for breaking the input scene into a set of objects, and object selection which allows one of the objects of the scene to be selected at a time. This object selection system has been applied to real gray-level and color images and the simulation results show the effectiveness of the system. (C) 2010 Elsevier Ltd. All rights reserved.

Taking advantage of contextualized interactions while users watch TV

While watching TV, viewers use the remote control to turn the TV set on and off, change channel and volume, to adjust the image and audio settings, etc. Worldwide, research institutes collect information about audience measurement, which can also be used to provide personalization and recommendation services, among others. The interactive digital TV offers viewers the opportunity to interact with interactive applications associated with the broadcast program. Interactive TV infrastructure supports the capture of the user-TV interaction at fine-grained levels. In this paper we propose the capture of all the user interaction with a TV remote control-including short term and instant interactions: we argue that the corresponding captured information can be used to create content pervasively and automatically, and that this content can be used by a wide variety of services, such as audience measurement, personalization and recommendation services. The capture of fine grained data about instant and interval-based interactions also allows the underlying infrastructure to offer services at the same scale, such as annotation services and adaptative applications. We present the main modules of an infrastructure for TV-based services, along with a detailed example of a document used to record the user-remote control interaction. Our approach is evaluated by means of a proof-of-concept prototype which uses the Brazilian Digital TV System, the Ginga-NCL middleware.

Cyclic Maximal Ideals of Rings of Differential Operators over Power Series Rings

In [3], Bratti and Takagi conjectured that a first order differential operator S=11 +...+ nn+ with 1,..., n, {x1,..., xn} does not generate a cyclic maximal left (or right) ideal of the ring of differential operators. This is contrary to the case of the Weyl algebra, i.e., the ring of differential operators over the polynomial ring [x1,..., xn]. In this case, we know that such cyclic maximal ideals do exist. In this article, we prove several special cases of the conjecture of Bratti and Takagi.

An evaluation of three upwinding approximations for numerical modeling the flow in tubular membrane of Newtonian and non-Newtonian fluids

In this paper, the laminar fluid flow of Newtonian and non-Newtonian of aqueous solutions in a tubular membrane is numerically studied. The mathematical formulation, with associated initial and boundary conditions for cylindrical coordinates, comprises the mass conservation, momentum conservation and mass transfer equations. These equations are discretized by using the finite-difference technique on a staggered grid system. Comparisons of the three upwinding schemes for discretization of the non-linear (convective) terms are presented. The effects of several physical parameters on the concentration profile are investigated. The numerical results compare favorably with experimental data and the analytical solutions. (C) 2011 Elsevier Inc. All rights reserved.

Modularity and robustness of bone networks

Cortical bones, essential for mechanical support and structure in many animals, involve a large number of canals organized in intricate fashion. By using state-of-the art image analysis and computer graphics, the 3D reconstruction of a whole bone (phalange) of a young chicken was obtained and represented in terms of a complex network where each canal was associated to an edge and every confluence of three or more canals yielded a respective node. The representation of the bone canal structure as a complex network has allowed several methods to be applied in order to characterize and analyze the canal system organization and the robustness. First, the distribution of the node degrees (i.e. the number of canals connected to each node) confirmed previous indications that bone canal networks follow a power law, and therefore present some highly connected nodes (hubs). The bone network was also found to be partitioned into communities or modules, i.e. groups of nodes which are more intensely connected to one another than with the rest of the network. We verified that each community exhibited distinct topological properties that are possibly linked with their specific function. In order to better understand the organization of the bone network, its resilience to two types of failures (random attack and cascaded failures) was also quantified comparatively to randomized and regular counterparts. The results indicate that the modular structure improves the robustness of the bone network when compared to a regular network with the same average degree and number of nodes. The effects of disease processes (e. g., osteoporosis) and mutations in genes (e.g., BMP4) that occur at the molecular level can now be investigated at the mesoscopic level by using network based approaches.

Mode of operation and low-resolution structure of a multi-domain and hyperthermophilic endo-beta-1,3-glucanase from Thermotoga petrophila

1,3-beta-Glucan depolymerizing enzymes have considerable biotechnological applications including biofuel production, feedstock-chemicals and pharmaceuticals. Here we describe a comprehensive functional characterization and low-resolution structure of a hyperthermophilic laminarinase from Thermotoga petrophila (TpLam). We determine TpLam enzymatic mode of operation, which specifically cleaves internal beta-1,3-glucosidic bonds. The enzyme most frequently attacks the bond between the 3rd and 4th residue from the non-reducing end, producing glucose, laminaribiose and laminaritriose as major products. Far-UV circular dichroism demonstrates that TpLam is formed mainly by beta structural elements, and the secondary structure is maintained after incubation at 90 degrees C. The structure resolved by small angle X-ray scattering, reveals a multi-domain structural architecture of a V-shape envelope with a catalytic domain flanked by two carbohydrate-binding modules. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved.

Density-Profile Processes Describing Biological Signaling Networks: Almost Sure Convergence to Deterministic Trajectories

We introduce jump processes in R(k), called density-profile processes, to model biological signaling networks. Our modeling setup describes the macroscopic evolution of a finite-size spin-flip model with k types of spins with arbitrary number of internal states interacting through a non-reversible stochastic dynamics. We are mostly interested on the multi-dimensional empirical-magnetization vector in the thermodynamic limit, and prove that, within arbitrary finite time-intervals, its path converges almost surely to a deterministic trajectory determined by a first-order (non-linear) differential equation with explicit bounds on the distance between the stochastic and deterministic trajectories. As parameters of the spin-flip dynamics change, the associated dynamical system may go through bifurcations, associated to phase transitions in the statistical mechanical setting. We present a simple example of spin-flip stochastic model, associated to a synthetic biology model known as repressilator, which leads to a dynamical system with Hopf and pitchfork bifurcations. Depending on the parameter values, the magnetization random path can either converge to a unique stable fixed point, converge to one of a pair of stable fixed points, or asymptotically evolve close to a deterministic orbit in Rk. We also discuss a simple signaling pathway related to cancer research, called p53 module.

On the Derived Categories and Quasitilted Algebras

In this paper, we present some results on the bounded derived category of Artin algebras, and in particular on the indecomposable objects in these categories, using homological properties. Given a complex X*, we consider the set J(X*) = {i is an element of Z vertical bar H(i)(X*) not equal 0} and we define the application l(X*) = maxJ(X*) - minJ(X*) + 1. We give relationships between some homological properties of an algebra and the respective application l. On the other hand, using homological properties again, we determine two subcategories of the bounded derived category of an algebra, which turn out to be the bounded derived categories of quasi-tilted algebras. As a consequence of these results we obtain new characterizations of quasi-tilted and quasi-tilted gentle algebras.

A NOTE ON THE COMPOSITE OF TWO IRREDUCIBLE MORPHISMS

In this note, we show that a composite of two irreducible morphisms between indecomposable modules cannot lie in R(3)\R(5).

A note on tilting sequences

We discuss the existence of tilting modules which are direct limits of finitely generated tilting modules over tilted algebras.

The bound quiver of a split extension

In this paper, we give a sufficient (which is also necessary under a compatibility hypothesis) condition on a set of arrows in the quiver of an algebra A so that A is a split extension of A/M, where M is the ideal of A generated by the classes of these arrows. We also compare the notion of split extension with that of semiconvex extension of algebras.

Torsion theories induced from commutative subalgebras

We begin a study of torsion theories for representations of finitely generated algebras U over a field containing a finitely generated commutative Harish-Chandra subalgebra Gamma. This is an important class of associative algebras, which includes all finite W-algebras of type A over an algebraically closed field of characteristic zero, in particular, the universal enveloping algebra of gl(n) (or sl(n)) for all n. We show that any Gamma-torsion theory defined by the coheight of the prime ideals of Gamma is liftable to U. Moreover, for any simple U-module M, all associated prime ideals of M in Spec Gamma have the same coheight. Hence, the coheight of these associated prime ideals is an invariant of a given simple U-module. This implies the stratification of the category of U-modules controlled by the coheight of the associated prime ideals of Gamma. Our approach can be viewed as a generalization of the classical paper by Block (1981) [4]; it allows, in particular, to study representations of gl(n) beyond the classical category of weight or generalized weight modules. (C) 2011 Elsevier B.V. All rights reserved.

ON THE COMPOSITE OF THREE IRREDUCIBLE MORPHISMS IN THE FOURTH POWER OF THE RADICAL

We study here the nonzero composite of three irreducible morphisms between indecomposable modules lying in the fourth power of the radical.

SEMIPERFECT IPRI-RINGS AND RIGHT BEZOUT RINGS

We present a survey of some results on ipri-rings and right Bezout rings. All these rings are generalizations of principal ideal rings. From the general point of view, decomposition theorems are proved for semiperfect ipri-rings and right Bezout rings.