Fernando Antoneli

The hidden factors in impact factors: a perspective from Brazilian science

Contrary to all current international recommendations on evaluation of academic achievement the evaluation of graduate programs in Brazil relies heavily on journal impact factors (Garfield, 2006; San Francisco Declaration on Research Assessment, 2013). The governmental agency CAPES from the Education Ministry monopolize this evaluation and pressure programs by the distribution of funding resources and departmental fellowships conditioned to adherence to a journal classification system called “Qualis” which is a discretization of the continuous distribution of journals ranking by their impact factors (Greenwood, 2007). In several institutions the graduate committee authorizes professors to act as thesis advisors only if in a certain period (e.g., 4 years) they publish at least one paper in a journal classified as “Qualis A2.” This classification has seven categories with decreasing impact factor ranges (A1, A2, B1, B2, B3, B4, B5, and C, http://www.capes.gov.br/avaliacao/qualis) and has certain percentile adjustments depending on the field of research. This has been hailed as a major cause for the enhancement of Brazilian scientific output although this system has several critics, demanding a profound review of evaluation criteria, and a proper adaptation to international guidelines (Rocha-e-Silva, 2009; Hermes-Lima, 2013). Most critics suggest that the excessive concern with publication in certain journals is in fact reducing the originality. Recently, to dismay of CAPES, a survey of the Brazilian science publication output, from 2001 to 2011, has shown that although Brazil has climbed from 17th place to 13th place in the total number of papers it has dropped from 31th to 40th place in citations (Rughetti, 2013).

Patterns of synchrony in lattice dynamical systems

From the point of view of coupled systems developed by Stewart, Golubitsky and Pivato, lattice differential equations consist of choosing a phase space Rk for each point in a lattice, and a system of differential equations on each of these spaces Rk such that the whole system is translation invariant. The architecture of a lattice differential equation specifies the sites that are coupled to each other (nearest neighbour coupling (NN) is a standard example). A polydiagonal is a finite-dimensional subspace of phase space obtained by setting coordinates in different phase spaces as equal. There is a colouring of the network associated with each polydiagonal obtained by colouring any two cells that have equal coordinates with the same colour. A pattern of synchrony is a colouring associated with a polydiagonal that is flow-invariant for every lattice differential equation with a given architecture. We prove that every pattern of synchrony for a fixed architecture in planar lattice differential equations is spatially doubly-periodic, assuming that the couplings are sufficiently extensive. For example, nearest and next nearest neighbour couplings are needed for square and hexagonal couplings, but a third level of coupling is needed for the corresponding result to hold in rhombic and primitive cubic lattices. On planar lattices this result is known to fail if the network architecture consists only of NN. The techniques we develop to prove spatial periodicity and finiteness can be applied to other lattices as well.

Invariants, equivariants and characters in symmetric bifurcation theory

In the analysis of stability in bifurcation problems it is often assumed that the (appropriate reduced) equations are in normal form. In the presence of symmetry, the truncated normal form is an equivariant polynomial map. Therefore, the determination of invariants and equivariants of the group of symmetries of the problem is an important step. In general, these are hard problems of invariant theory and, in most cases, they are tractable only through symbolic computer programs. Nevertheless, it is desirable to obtain some of the information about invariants and equivariants without actually computing them, for example, the number of linearly independent homogeneous invariants or equivariants of a certain degree. Generating functions for these dimensions are generally known as ‘Molien functions’. We obtain formulae for the number of linearly independent homogeneous invariants or equivariants for Hopf bifurcation in terms of characters. We also show how to construct Molien functions for invariants and equivariants for Hopf bifurcation. Our results are then applied to the computation of the number of invariants and equivariants for Hopf bifurcation for several finite groups and the continuous group O(3).

EXTENDING THE SEARCH FOR SYMMETRIES IN THE GENETIC CODE

We report on the search for symmetries in the genetic code involving the medium rank simple Lie algebras

ON AMINO ACID AND CODON ASSIGNMENT IN ALGEBRAIC MODELS FOR THE GENETIC CODE

B_6 = {\mathfrak{so}}(13)

Symmetry breaking in the genetic code: Finite groups

and

A Model of Gene Expression Based on Random Dynamical Systems Reveals Modularity Properties of Gene Regulatory Networks

D_7 = {\mathfrak {so}}(14)

Protein synthesis driven by dynamical stochastic transcription

, in the context of the algebraic approach originally proposed by one of the present authors, which aims at explaining the degeneracies encountered in the genetic code as the result of a sequence of symmetry breakings that have occurred during its evolution.

Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage

We give a list of all possible schemes for performing amino acid and codon assignments in algebraic models for the genetic code, which are consistent with a few simple symmetry principles, in accordance with the spirit of the algebraic approach to the evolution of the genetic code proposed by Hornos and Hornos. Our results are complete in the sense of covering all the algebraic models that arise within this approach, whether based on Lie groups/Lie algebras, on Lie superalgebras or on finite groups.

HIV-1 Tropism Determines Different Mutation Profiles in Proviral DNA

We investigate the possibility of interpreting the degeneracy of the genetic code, i.e., the feature that different codons (base triplets) of DNA are transcribed into the same amino acid, as the result of a symmetry breaking process, in the context of finite groups. In the first part of this paper, we give the complete list of all codon representations (64-dimensional irreducible representations) of simple finite groups and their satellites (central extensions and extensions by outer automorphisms). In the second part, we analyze the branching rules for the codon representations found in the first part by computational methods, using a software package for computational group theory. The final result is a complete classification of the possible schemes, based on finite simple groups, that reproduce the multiplet structure of the genetic code.