Generalizations of the genomic rank distance to indels

MOTIVATION: The rank distance model represents genome rearrangements in multi-chromosomal genomes as matrix operations, which allows the reconstruction of parsimonious histories of evolution by rearrangements. We seek to generalize this model by allowing for genomes with different gene content, to accommodate a broader range of biological contexts. We approach this generalization by using a matrix representation of genomes. This leads to simple distance formulas and sorting algorithms for genomes with different gene contents, but without duplications. RESULTS: We generalize the rank distance to genomes with different gene content in two different ways. The first approach adds insertions, deletions and the substitution of a single extremity to the basic operations. We show how to efficiently compute this distance. To avoid genomes with incomplete markers, our alternative distance, the rank-indel distance, only uses insertions and deletions of entire chromosomes. We construct phylogenetic trees with our distances and the DCJ-Indel distance for simulated data and real prokaryotic genomes, and compare them against reference trees. For simulated data, our distances outperform the DCJ-Indel distance using the Quartet metric as baseline. This suggests that rank distances are more robust for comparing distantly related species. For real prokaryotic genomes, all rearrangement-based distances yield phylogenetic trees that are topologically distant from the reference (65% similarity with Quartet metric), but are able to cluster related species within their respective clades and distinguish the Shigella strains as the farthest relative of the Escherichia coli strains, a feature not seen in the reference tree. AVAILABILITY AND IMPLEMENTATION: Code and instructions are available at https://github.com/meidanis-lab/rank-indel. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Mesenteric panniculitis

A 68 years old male patient presented with recurrent abdominal pain and with a palpable mas

H? robust memory controllers for networked control systems: uncertain sampling rates and time delays in polytopic domains

In this paper, the problem of controller design for networked control systems with time-varying sampling rates and time delays is investigated. By using a memory at the feedback loop, a digital robust controller that minimizes an upper bound to the Hinfin performance of the closed loop system is determined. The design conditions are obtained from the Finsler\u27s Lemma combined with the Lyapunov theory and expressed in terms of bilinear matrix inequalities. Extra variables introduced by the Finsler\u27s Lemma are explored in order to provide a better system behavior. The time-varying uncertainties are modelled using polytopic domains. The controller is obtained by the solution of an optimization problem formulated only in terms of the vertices of the polytope, avoiding grids in the parametric space. Numerical examples illustrate the efficiency of the proposed approach

H? filtering of time-varying systems with bounded rates of variation

In this paper, the problem of robust filter design for time-varying discrete-time polytopic systems with bounded rates of variation is investigated. The design conditions are obtained by using a parameter-dependent Lyapunov function and the Finsler\u27s Lemma. A robust filter, that minimizes an upper bound to the H? performance of the estimation error, is obtained as the solution of an optimization problem. A more precise geometric representation of the parameter time variation was used in order to obtain less conservative design conditions. Robust filters for time-invariant, as well as arbitrarily time-varying, polytopic systems can be obtained as a particular case of the proposed method. Numerical examples illustrate the results

H? Gain Scheduling for Discrete-Time Systems with Control Delays and Time-Varying Parameters: a BMI Approach

In this paper, the problem of gain scheduling for time-varying systems with time delays is investigated. By using a memory at the feedback loop, a discrete gain scheduled controller which minimizes an upper bound to the ,Hscrinfin performance of the closed loop system is determined. The design conditions, expressed in terms of bilinear matrix inequalities, are obtained from the Finsler\u27s Lemma combined with the Lyapunov theory. The extra variables introduced by the Finsler\u27s Lemma represent an alternative way in the search of better system behavior. The time-varying uncertainties are modeled using polytopic domains. The controller is obtained by the solution of an optimization problem formulated only in terms of the vertices of the polytope. No grids in the parametric space are used. Numerical examples illustrate the efficiency of the proposed approach

Transcription of Aspergillus nidulans pacC is modulated by alternative RNA splicing of palB

AbstractFungi have evolved elaborate signal transduction networks for remodeling metabolic pathways to scavenge nutrients, including the secretion of nutritional enzymes. This adaptive response involves the conserved PacC/Pal signal transduction pathway, which mediates the transcriptional response to ambient pH. In this study, we show that transcription of the gene for PacC is modulated in response to nutrient changes, phosphate and carbon sources, and pH. In addition, we show that transcription of pacC is modulated in response to alternative RNA splicing of the palB gene. These results reveal novel aspects of the complex network involved in modulation of pacC

Degradação de compostos fenólicos por estirpes de Lactobacillus isoladas de águas russas

Comunicação apresentada no III Simpósio Nacional de Olvicultura que decorreu em Castelo Branco, na Escola Superior Agrária do Instituto Politécnico de Castelo Branco, de 289 a 31 de Outubro de 2003.As águas russas, principal resíduo da indústria de extracção do azeite, são caracterizadas por uma elevada carga orgânica poluente constituindo, por esta razão, um dos mais graves problemas ambientais dos países da bacia mediterrânea. São particularmente ricas em compostos fenólicos, lípidos e açúcares e apresentam teores mínimos de compostos azotados. O seu potencial biológico e energético é importante, pelo que se estudou a possibilidade de serem usadas como meio de cultura para produção de inóculos lácticos para a indústria de preparação de azeitona de mesa. Foram estudadas várias fontes de compensação de azoto, bem como vários tipos de meio, líquido ou sistema bifásico, com vista à maximização da capacidade de degradação de compostos fenólicos por bactérias lácticas (BL). Foram também estudados alguns dos factores de adaptação das BL às condições de stress fenólico. Concluiu-se que a degradação dos compostos fenólicos e a produção de ácido láctico depende do tipo e da concentração de azoto. Verificou-se que as BL possuem um mecanismo de adaptação ao stress fenólico, baseado em alterações dos seus componentes celulares

Convex relaxations with guaranteed convergence for control design of takagi-sugeno fuzzy systems

This paper provides convex conditions with certificates of convergence for the design of state feedback controllers that quadratically stabilize and also ensure optimal H2 and H∞ performances under quadratic stability for Takagi-Sugeno continuous-time fuzzy systems. The proposed conditions are formulated as parameter-dependent linear matrix inequalities (LMIs) that have extra variables from Finsler's lemma and parameters belonging to the unit simplex. The fuzzy control law is written as a state feedback gain that is a homogeneous polynomial of degree g, encompassing the parallel distributed compensator as a special case when g = 1. Algebraic properties of the system parameters and recent results of positive polynomials are used to construct LMI relaxations which, differently from most relaxations in the literature, asymptotically converge to a solution whenever such solution exists. Due to the degree of freedom obtained with the extra variables, the conditions presented in the paper are an improvement over earlier results based on Pólya's theorem and can be viewed as an alternative to the use of techniques based on the relaxation of quadratic forms. The numerical efficiency in terms of precision and computational effort is demonstrated by means of comparisons with other methods from the literature.Este artigo fornece condições convexas com convergência garantida para o projeto de controladores por realimentação de estados que estabilizam quadraticamente e também asseguram desempenhos ótimos H2 e H∞ sob estabilidade quadrática para sistemas nebulosos de Takagi-Sugeno contínuos no tempo. As condições propostas são formuladas como desigualdades matriciais lineares (LMIs) dependentes de parâmetros com variáveis de folga provenientes do Lema de Finsler e com parâmetros pertencentes ao simplex unitário. A lei de controle nebulosa é dada por um ganho de realimentação de estados que é um polinômio homogêneo de grau g, que tem como caso particular o compensador paralelo distribuído quando g = 1. Propriedades algébricas dos parâmetros do sistema e resultados recentes sobre positividade de polinômios são usados para construir relaxações LMIs que, diferentemente da maioria das relaxações da literatura, convergem assintoticamente para a solução sempre que esta existir. Graças ao grau de liberdade obtido pelo uso de variáveis de folga, as condições apresentadas no artigo representam avanços em relação a condições recentemente publicadas baseadas no Teorema de Pólya, e podem ser vistas como uma alternativa a técnicas baseadas na relaxação de formas quadráticas. A eficiência numérica em termos de precisão e esforço computacional é demonstrada por meio de comparações com outros métodos da literatura.8295Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES