BackgroundThe distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of such markers. In these models, a deletion and a subsequent insertion that occur at the same position of the genome count for two sorting steps.ResultsHere we propose a new model that sorts non-common markers with substitutions, which are more powerful operations that comprehend insertions and deletions. A deletion and an insertion that occur at the same position of the genome can be modeled as a substitution, counting for a single sorting step.ConclusionsComparing genomes with unequal content, but without duplicated markers, we give a linear time algorithm to compute the genomic distance considering substitutions and double-cut-and-join (DCJ) operations. This model provides a parsimonious genomic distance to handle genomes free of duplicated markers, that is in practice a lower bound to the real genomic distances. The method could also be used to refine orthology assignments, since in some cases a substitution could actually correspond to an unannotated orthology.
Scientific and other non-patent references (NPRs) in patents are important tools to analyze interactions between science and technology. This paper organizes a database with 514,894 USPTO patents granted globally in 1974, 1982, 1990, 1998 and 2006. There are 165,762 patents with at least one reference to science and engineering (S&E) literature, from a total of 1,375,503 references. Through a lexical analysis, 71.1% of this S&E literature is classified by S&E fields. These data serve as the basis for the elaboration of global and national 3-dimensional matrices (technological domains, S&E fields and number of references). Three indicators are proposed to analyze these matrices, allowing us to identify patterns of structured growth that differentiate developed and non-developed countries. This differentiation informs suggestions for public policies for development, emphasizing the need for an articulation between the industrial and technological dimension and scientific side. The intertwinement of these two dimensions is a key component of developmental policies for the twenty-first century.
BackgroundClassical approaches to compute the genomic distance are usually limited to genomes with the same content, without duplicated markers. However, differences in the gene content are frequently observed and can reflect important evolutionary aspects. A few polynomial time algorithms that include genome rearrangements, insertions and deletions (or substitutions) were already proposed. These methods often allow a block of contiguous markers to be inserted, deleted or substituted at once but result in distance functions that do not respect the triangular inequality and hence do not constitute metrics.ResultsIn the present study we discuss the disruption of the triangular inequality in some of the available methods and give a framework to establish an efficient correction for two models recently proposed, one that includes insertions, deletions and double cut and join (DCJ) operations, and one that includes substitutions and DCJ operations.ConclusionsWe show that the proposed framework establishes the triangular inequality in both distances, by summing a surcharge on indel operations and on substitutions that depends only on the number of markers affected by these operations. This correction can be applied a posteriori, without interfering with the already available formulas to compute these distances. We claim that this correction leads to distances that are biologically more plausible.
This paper presents a new methodology to describe global innovations networks. Using 167,315 USPTO patents granted in 2009 and the papers they cited, this methodology shows ''scientific footprints of technology'' that cross national boundaries, and how multinational enterprises interact globally with universities and other firms. The data and the map of these flows provide insights to support a tentative taxonomy of global innovation networks.
One of the most intriguing features of the immune system is regulation: a limited response when perturbed repeatedly. We propose a minimal network model for immune regulation in a lymphocyte network containing two types of elements: B lymphocytes and ligands that bind to their receptors. Effective interactions between B cells, mediated by other components of the immune system can be excitatory or inhibitory. In our model, B cell clones and ligand species are represented by nodes, and interactions by links. We expect that, as in many complex systems, the connectivity distribution is broad, motivating study of the model on a scale-free network; for comparison we study the same dynamics on a random graph. We characterize the dynamics of the model and its response to perturbations. Our model reproduces several key features of immune system dynamics: regulation (saturation of response), and more rapid response upon repeated perturbation with the same agents. Our results suggest that a scale-free network of interactions contributes to the regulation and dynamics of the immune system.
There are new reasons for revisiting Marx's elaboration on the rate of profit because contemporary debates provide findings from the MEGA Project, long-term data on the rate of profit, and tools for dealing with complexity and non-equilibrium systems. This article proposes that the interplay between the tendency and the countertendencies of the rate of profit to fall can be translated into a simple system of equations, one based on each chapter of Section III of Capital-as if Marx sought to mathematically formalise his insights. This article reviews previous debates, presents data and runs a simulation model, showing that the rate of profit behaves as fractals. ARTICLE HISTORYrate of profit to fall and its countertendencies. This insight from his writings of 1863-5 can now be tested against evidence on the behaviour of the rate of profit in the last 150 years.The contribution of this article is the suggestion that the interplay between the tendency and the countertendencies (Callinicos 2014, p. 270) can be translated into a very simple system of equations. This system of equations is an attempt to model the long-term behaviour of the rate of profit. More specifically, each chapter of Section III of Das Kapital may be transformed into one equation, as if Marx was preparing to mathematically formalise his insights. This system of equations will push us to a non-linear world. Accordingly, this article applies tools of non-linear mathematics and complexity to, through simulations, try to replicate and evaluate these long-term dynamics.A short literature review on the debates related to the profit rate is the subject of the second section of this article. This review indicates the specific contribution of Marx vis-à-vis classical economists, summarises the three rounds of debate regarding the rate of profit in the history of economic thought, and shows how this subject permeates modern economics.This second section hints at elements of complexity in the behaviour of the profit rate. The third section then summarises a short history of complexity and non-linear mathematics. This gives the reader some familiarity with the necessary tools to describe the long-term behaviour of the profit rate. A fourth section discusses the role of countertendencies in the history of capitalism and empirically evaluates the long-term behaviour of the profit rate, based on data for the last 150 years of the United States (US). It also conducts a preliminary analysis of the non-linear properties of this behaviour. The fifth section combines the two strands of analysis reviewed in sections Two and Three, suggesting a translation of Marx's insights on the interplay between the tendency for the rate of profit to fall and its counter-tendencies into a system of equations. This system of equations feeds a simulation model that is implemented to test the ability of those equations to replicate the long-term dynamics of the rate of profit in a capitalist economy. A final section presents the implications of this analysis and evaluates the results...
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