Cheaters in mutualism networks

Mutualism-network studies assume that all interacting species are mutualistic partners and consider that all links are of one kind. However, the influence of different types of links, such as cheating links, on network organization remains unexplored. We studied two flower-visitation networks (Malpighiaceae and Bignoniaceae and their flower visitors), and divide the types of link into cheaters (i.e. robbers and thieves of flower rewards) and effective pollinators. We investigated if there were topological differences among networks with and without cheaters, especially with respect to nestedness and modularity. The Malpighiaceae network was nested, but not modular, and it was dominated by pollinators and had much fewer cheater species than Bignoniaceae network (28% versus 75%). The Bignoniaceae network was mainly a plant-cheater network, being modular because of the presence of pollen robbers and showing no nestedness. In the Malpighiaceae network, removal of cheaters had no major consequences for topology. In contrast, removal of cheaters broke down the modularity of the Bignoniaceae network. As cheaters are ubiquitous in all mutualisms, the results presented here show that they have a strong impact upon network topology.

Analysis of a hyper-diverse seed dispersal network: modularity and underlying mechanisms

Mutualistic interactions involving pollination and ant-plant mutualistic networks typically feature tightly linked species grouped in modules. However, such modularity is infrequent in seed dispersal networks, presumably because research on those networks predominantly includes a single taxonomic animal group (e.g. birds). Herein, for the first time, we examine the pattern of interaction in a network that includes multiple taxonomic groups of seed dispersers, and the mechanisms underlying modularity. We found that the network was nested and modular, with five distinguishable modules. Our examination of the mechanisms underlying such modularity showed that plant and animal trait values were associated with specific modules but phylogenetic effect was limited. Thus, the pattern of interaction in this network is only partially explained by shared evolutionary history. We conclude that the observed modularity emerged by a combination of phylogenetic history and trait convergence of phylogenetically unrelated species, shaped by interactions with particular types of dispersal agents.

The Evolution of Modularity in the Mammalian Skull I: Morphological Integration Patterns and Magnitudes

Morphological integration refers to the modular structuring of inter-trait relationships in an organism, which could bias the direction and rate of morphological change, either constraining or facilitating evolution along certain dimensions of the morphospace. Therefore, the description of patterns and magnitudes of morphological integration and the analysis of their evolutionary consequences are central to understand the evolution of complex traits. Here we analyze morphological integration in the skull of several mammalian orders, addressing the following questions: are there common patterns of inter-trait relationships? Are these patterns compatible with hypotheses based on shared development and function? Do morphological integration patterns and magnitudes vary in the same way across groups? We digitized more than 3,500 specimens spanning 15 mammalian orders, estimated the correspondent pooled within-group correlation and variance/covariance matrices for 35 skull traits and compared those matrices among the orders. We also compared observed patterns of integration to theoretical expectations based on common development and function. Our results point to a largely shared pattern of inter-trait correlations, implying that mammalian skull diversity has been produced upon a common covariance structure that remained similar for at least 65 million years. Comparisons with a rodent genetic variance/covariance matrix suggest that this broad similarity extends also to the genetic factors underlying phenotypic variation. In contrast to the relative constancy of inter-trait correlation/covariance patterns, magnitudes varied markedly across groups. Several morphological modules hypothesized from shared development and function were detected in the mammalian taxa studied. Our data provide evidence that mammalian skull evolution can be viewed as a history of inter-module parcellation, with the modules themselves being more clearly marked in those lineages with lower overall magnitude of integration. The implication of these findings is that the main evolutionary trend in the mammalian skull was one of decreasing the constraints to evolution by promoting a more modular architecture.

Upgrading a TCABR data analysis and acquisition system for remote participation using Java, XML, RCP and modern client/server communication/authentication

The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The architecture of the new system uses Java language as programming environment. Since application parameters and hardware in a joint experiment are complex with a large variability of components, requirements and specification solutions need to be flexible and modular, independent from operating system and computer architecture. To describe and organize the information on all the components and the connections among them, systems are developed using the extensible Markup Language (XML) technology. The communication between clients and servers uses remote procedure call (RPC) based on the XML (RPC-XML technology). The integration among Java language, XML and RPC-XML technologies allows to develop easily a standard data and communication access layer between users and laboratories using common software libraries and Web application. The libraries allow data retrieval using the same methods for all user laboratories in the joint collaboration, and the Web application allows a simple graphical user interface (GUI) access. The TCABR tokamak team in collaboration with the IPFN (Instituto de Plasmas e Fusao Nuclear, Instituto Superior Tecnico, Universidade Tecnica de Lisboa) is implementing this remote participation technologies. The first version was tested at the Joint Experiment on TCABR (TCABRJE), a Host Laboratory Experiment, organized in cooperation with the IAEA (International Atomic Energy Agency) in the framework of the IAEA Coordinated Research Project (CRP) on ""Joint Research Using Small Tokamaks"". (C) 2010 Elsevier B.V. All rights reserved.

Exclusive processes in electron-ion collisions

The exclusive processes in electron-ion (eA) interactions are an important tool to investigate the QCD dynamics at high energies as they are in general driven by the gluon content of the target which is strongly subject to parton saturation effects. In this Letter we compute the cross sections for the exclusive vector meson production as well as the deeply virtual Compton scattering (DVCS) relying on the color dipole approach and considering the numerical solution of the Balitsky-Kovchegov equation including running coupling corrections (rcBK). The production cross sections obtained with the rcBK solution and bCGC parametrization are very similar, the former being slightly larger. (C) 2011 Elsevier B.V. All rights reserved.

Antihyperon polarization in high-energy inclusive processes

We propose a model for the antihyperon polarization in high-energy proton-nucleus inclusive reactions, based on the final-state interactions between the antihyperons and other produced particles (predominantly pions). To formulate this idea, we use the previously obtained low-energy pion-(anti-)hyperon interaction using effective chiral Lagrangians, and a hydrodynamic parametrization of the background matter, which expands and decouples at a certain freezeout temperature.

Investigating relationships within and between category networks in Wikipedia

This work maps and analyses cross-citations in the areas of Biology, Mathematics, Physics and Medicine in the English version of Wikipedia, which are represented as an undirected complex network where the entries correspond to nodes and the citations among the entries are mapped as edges. We found a high value of clustering coefficient for the areas of Biology and Medicine, and a small value for Mathematics and Physics. The topological organization is also different for each network, including a modular structure for Biology and Medicine, a sparse structure for Mathematics and a dense core for Physics. The networks have degree distributions that can be approximated by a power-law with a cut-off. The assortativity of the isolated networks has also been investigated and the results indicate distinct patterns for each subject. We estimated the betweenness centrality of each node considering the full Wikipedia network, which contains the nodes of the four subjects and the edges between them. In addition, the average shortest path length between the subjects revealed a close relationship between the subjects of Biology and Physics, and also between Medicine and Physics. Our results indicate that the analysis of the full Wikipedia network cannot predict the behavior of the isolated categories since their properties can be very different from those observed in the full network. (C) 2011 Elsevier Ltd. 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.

Identifying the borders of mathematical knowledge

Based on a divide and conquer approach, knowledge about nature has been organized into a set of interrelated facts, allowing a natural representation in terms of graphs: each `chunk` of knowledge corresponds to a node, while relationships between such chunks are expressed as edges. This organization becomes particularly clear in the case of mathematical theorems, with their intense cross-implications and relationships. We have derived a web of mathematical theorems from Wikipedia and, thanks to the powerful concept of entropy, identified its more central and frontier elements. Our results also suggest that the central nodes are the oldest theorems, while the frontier nodes are those recently added to the network. The network communities have also been identified, allowing further insights about the organization of this network, such as its highly modular structure.

Linear covariant gauges on the lattice

Linear covariant gauges, such as Feynman gauge, are very useful in perturbative calculations. Their non-perturbative formulation is, however, highly non-trivial. In particular, it is a challenge to define linear covariant gauges on a lattice. We consider a class of gauges in lattice gauge theory that coincides with the perturbative definition of linear covariant gauges in the formal continuum limit. The corresponding gauge-fixing procedure is described and analyzed in detail, with an application to the pure SU(2) case. In addition, results for the gluon propagator in the two-dimensional case are given. (C) 2008 Elsevier B.V. All rights reserved.

Approximations of modal logics: K and beyond

Inspired by the recent work on approximations of classical logic, we present a method that approximates several modal logics in a modular way. Our starting point is the limitation of the n-degree of introspection that is allowed, thus generating modal n-logics. The semantics for n-logics is presented, in which formulas are evaluated with respect to paths, and not possible worlds. A tableau-based proof system is presented, n-SST, and soundness and completeness is shown for the approximation of modal logics K, T, D, S4 and S5. (c) 2008 Published by Elsevier B.V.

Nuclear elements of degree 6 in the free alternative algebra

We construct five new elements of degree 6 in the nucleus of the free alternative algebra. We use the representation theory of the symmetric group to locate the elements. We use the computer algebra system ALBERT and an extension of ALBERT to express the elements in compact form and to show that these new elements are not a consequence of the known clegree-5 elements in the nucleus. We prove that these five new elements and four known elements form a basis for the subspace of nuclear elements of degree 6. Our calculations are done using modular arithmetic to save memory and time. The calculations can be done in characteristic zero or any prime greater than 6, and similar results are expected. We generated the nuclear elements using prime 103. We check our answer using five other primes.

Nil graded self-similar algebras

In [19], [24] we introduced a family of self-similar nil Lie algebras L over fields of prime characteristic p > 0 whose properties resemble those of Grigorchuk and Gupta-Sidki groups. The Lie algebra L is generated by two derivations v(1) = partial derivative(1) + t(0)(p-1) (partial derivative(2) + t(1)(p-1) (partial derivative(3) + t(2)(p-1) (partial derivative(4) + t(3)(p-1) (partial derivative(5) + t(4)(p-1) (partial derivative(6) + ...))))), v(2) = partial derivative(2) + t(1)(p-1) (partial derivative(3) + t(2)(p-1) (partial derivative(4) + t(3)(p-1) (partial derivative(5) + t(4)(p-1) (partial derivative(6) + ...)))) of the truncated polynomial ring K[t(i), i is an element of N vertical bar t(j)(p) =0, i is an element of N] in countably many variables. The associative algebra A generated by v(1), v(2) is equipped with a natural Z circle plus Z-gradation. In this paper we show that for p, which is not representable as p = m(2) + m + 1, m is an element of Z, the algebra A is graded nil and can be represented as a sum of two locally nilpotent subalgebras. L. Bartholdi [3] andYa. S. Krylyuk [15] proved that for p = m(2) + m + 1 the algebra A is not graded nil. However, we show that the second family of self-similar Lie algebras introduced in [24] and their associative hulls are always Z(p)-graded, graded nil, and are sums of two locally nilpotent subalgebras.

A matrix formula for the skewness of maximum likelihood estimators

We give a general matrix formula for computing the second-order skewness of maximum likelihood estimators. The formula was firstly presented in a tensorial version by Bowman and Shenton (1998). Our matrix formulation has numerical advantages, since it requires only simple operations on matrices and vectors. We apply the second-order skewness formula to a normal model with a generalized parametrization and to an ARMA model. (c) 2010 Elsevier B.V. All rights reserved.

Solvatochromic Shift of the pi -> pi* Transition in All-Trans, Cis-13, Cis-11, Cis-9, and Cis-7 Retinal Isomers Induced by Water and Methanol

The solvatochromic shift of the lowest singlet it pi -> pi* electronic transition in the all-trans, cis-13, cis-11, cis-9, and cis-7 retinal isomers were computed under the influence of water, methanol, and benzene solvents. Excitation energies were calculated in gas phase and in solution. The calculations in solution were performed considering the sequential Monte Carlo (MC) /Quantum Mechanical approach. The MC simulations were performed considering the full retinal isomer molecules and 900 water molecules, 900 methanol, or 400 benzene ones. The OPLS/AA parametrization was chosen for retinal, methanol, and benzene molecules and the SPC model was used for water one. From the MC calculations 100 independent configurations were selected, with 100 solvent molecules in thermodynamical equilibrium at T = 298.15 K. Average point-charges were obtained from those independent configurations for water, methanol, and benzene solvent. TDDFT and CASSCF//CASPT2 methodologies were used to compute the vertical excitation energy of the retinal isomers in different environment. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110: 2076-2087, 2010