113 research outputs found
The interface for functions in the dune-functions module
The dune-functions dune module introduces a new programmer interface for discrete and non-discrete functions. Unlike the previous interfaces considered in the existing dune modules, it is based on overloading operator(), and returning values by-value. This makes user code much more readable, and allows the incorporation of newer C++ features such as lambda expressions. Run-time polymorphism is implemented not by inheritance, but by type erasure, generalizing the ideas of the std::function class from the C++11 standard library. We describe the new interface, show its possibilities, and measure the performance impact of type erasure and return-by-value
Function space bases in the dune-functions module
The dune-functions Dune module provides interfaces for functions and function space bases. It forms one abstraction level above grids, shape functions, and linear algebra, and provides infrastructure for full discretization frameworks like dune-pdelab and dune-fem. This document describes the function space bases provided by dune-functions. These are based on an abstract description of bases for product spaces as trees of simpler bases. From this description, many different numberings of degrees of freedom by multi-indices can be derived in a natural way. We describe the abstract concepts, document the programmer interface, and give a complete example program that solves the stationary Stokes equation using Taylor-Hood elements
The structure of coevolving infection networks
Disease awareness in infection dynamics can be modeled with adaptive contact
networks whose rewiring rules reflect the attempt by susceptibles to avoid
infectious contacts. Simulations of this type of models show an active phase
with constant infected node density in which the interplay of disease dynamics
and link rewiring prompts the convergence towards a well defined degree
distribution, irrespective of the initial network topology. We develop a method
to study this dynamic equilibrium and give an analytic description of the
structure of the characteristic degree distributions and other network
measures. The method applies to a broad class of systems and can be used to
determine the steady-state topology of many other adaptive networks.Comment: Typo corrected in the last term of Eq.(2). Definition of
P_S(x,y,t|x_0,y_0) changed to allow for correct normalization in Eq.(5),
consequently \hat{P}_I=r*P_I instead of \hat{P}_I=P_I. All subsequent
formulae, results and conclusions in the original paper remain unaffecte
Evolution of CDC42, a putative virulence factor triggering meristematic growth in black yeasts
New insights in dermatophyte research
Dermatophyte research has renewed interest because of changing human floras with changing socioeconomic conditions, and because of severe chronic infections in patients with congenital immune disorders. Main taxonomic traits at the generic level have changed considerably, and now fine-tuning at the species level with state-of-the-art technology has become urgent. Research on virulence factors focuses on secreted proteases now has support in genome data. It is speculated that most protease families are used for degrading hard keratin during nitrogen recycling in the environment, while others, such as Sub6 may have emerged as a result of ancestral gene duplication, and are likely to have specific roles during infection. Virulence may differ between mating partners of the same species and concepts of zoo- and anthropophily may require revision in some recently redefined species. Many of these questions benefit from international cooperation and exchange of materials. The aim of the ISHAM Working Group Dermatophytes aims to stimulate and coordinate international networking on these fungi
Different reactions to adverse neighborhoods in games of cooperation
In social dilemmas, cooperation among randomly interacting individuals is
often difficult to achieve. The situation changes if interactions take place in
a network where the network structure jointly evolves with the behavioral
strategies of the interacting individuals. In particular, cooperation can be
stabilized if individuals tend to cut interaction links when facing adverse
neighborhoods. Here we consider two different types of reaction to adverse
neighborhoods, and all possible mixtures between these reactions. When faced
with a gloomy outlook, players can either choose to cut and rewire some of
their links to other individuals, or they can migrate to another location and
establish new links in the new local neighborhood. We find that in general
local rewiring is more favorable for the evolution of cooperation than
emigration from adverse neighborhoods. Rewiring helps to maintain the diversity
in the degree distribution of players and favors the spontaneous emergence of
cooperative clusters. Both properties are known to favor the evolution of
cooperation on networks. Interestingly, a mixture of migration and rewiring is
even more favorable for the evolution of cooperation than rewiring on its own.
While most models only consider a single type of reaction to adverse
neighborhoods, the coexistence of several such reactions may actually be an
optimal setting for the evolution of cooperation.Comment: 12 pages, 5 figures; accepted for publication in PLoS ON
Evolution of CDC42, a putative virulence factor triggering meristematic growth in black yeasts
The cell division cycle gene (CDC42) controlling cellular
polarization was studied in members of Chaetothyriales. Based on
ribosomal genes, ancestral members of the order exhibit meristematic growth in
view of their colonization of inert surfaces such as rock, whereas in derived
members of the order the gene is a putative virulence factor involved in
expression of the muriform cell, the invasive phase in human
chromoblastomycosis. Specific primers were developed to amplify a portion of
the gene of 32 members of the order with known position according to ribosomal
phylogeny. Phylogeny of CDC42 proved to be very different. In all
members of Chaetohyriales the protein sequence is highly conserved.
In most species, distributed all over the phylogenetic tree, introns and
3rd codon positions are also invariant. However, a number of
species had paralogues with considerable deviation in non-coding exon
positions, and synchronous variation in introns, although non-synonomous
variation had remained very limited. In some strains both orthologues and
paralogues were present. It is concluded that CDC42 does not show any
orthologous evolution, and that its paralogues haves the same function but are
structurally relaxed. The variation or absence thereof could not be linked to
ecological changes, from rock-inhabiting to pathogenic life style. It is
concluded that eventual pathogenicity in Chaetothyriales is not
expressed at the DNA level in CDC42 evolution
Network Economics and the Environment: Insights and Perspectives
Local interactions and network structures appear to be a prominent feature of many environmental problems. This paper discusses a wide range of issues and potential areas of application, including the role of relational networks in the pattern of adoption of green technologies, common pool resource problems characterized by a multiplicity of sources, the role of social networks in multi-level environmental governance, infrastructural networks in the access to and use of natural resources such as oil and natural gas, the use of networks to describe the internal structure of inter-country relations in international agreements, and the formation of bilateral "links" in the process of building up an environmental coalition. For each of these areas, we examine why and how network economics would be an effective conceptual and analytical tool, and discuss the main insights that we can foresee
Changes in frequency of agents of tinea capitis in school children from Western China suggest slow migration rates in dermatophytes
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