Feature selection environment for genomic applications

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Outdoor Cultivation of the Microalga Chlorella vulgaris in a New Photobioreactor Configuration: The Effect of Ultraviolet and Visible Radiation

Microalgae can be a future source of biomass with a wide range of applications, including its use to solve current environmental issues. One of the main variables for microalgal cultivation is the light supply: (i) its intensity that often does not present a uniform spatial distribution inside the culture; (ii) photoperiod; and (iii) spectrum. Therefore, this study aims to evaluate the growth of the microalgae Chlorella vulgaris in a tubular photobioreactor with compound parabolic collectors (CPCs) under outdoor conditions. The effect of ultraviolet and visible radiation on biomass productivity and nutrients (nitrogen and phosphorus) uptake was assessed. The maximum biomass productivity was (5 +/- 1) x 10(-3) g.L-1.h(-1), and the specific growth rates ranged from (1.1 +/- 0.3) x 10(-2) to (2.0 +/- 0.6) x 10(-2) h(-1). Regarding nutrient uptake, initial removal rates of (0.9 +/- 0.4) mg N.L-1.h(-1) for nitrogen and (0.17 +/- 0.04) mg P.L-1.h(-1) for phosphorus were reached. These values increased with visible and ultraviolet irradiance until certain values (143 W-VIS.m(-2) and 9 W-UV.m(-2) for biomass productivity; 101 W-VIS.m(-2) and 6 W-UV.m(-2) for nutrient removal) and then decreased for higher ones due to the photoinhibition phenomenon. Therefore, the application of CPCs to photobioreactors (PBRs) may be beneficial for microalgal culture in countries with higher latitude (with lower solar irradiance levels)

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.Fundacao de Amparo e Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Coordenacao de Aperfeicofamento de Pessoal de Nivel Superior (CAPES)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq

Identification of furfural resistant strains of Saccharomyces cerevisiae and Saccharomyces paradoxus from a collection of environmental and industrial isolates

Background Fermentation of bioethanol using lignocellulosic biomass as a raw material provides a sustainable alternative to current biofuel production methods by utilising waste food streams as raw material. Before lignocellulose can be fermented it requires physical, chemical and enzymatic treatment in order to release monosaccharides, a process that causes the chemical transformation of glucose and xylose into the cyclic aldehydes furfural and hydroxyfurfural. These furan compounds are potent inhibitors of Saccharomyces fermentation, and consequently furfural tolerant strains of Saccharomyces are required for lignocellulosic fermentation. Results This study investigated yeast tolerance to furfural and hydroxyfurfural using a collection of 71 environmental and industrial isolates of the baker’s yeast Saccharomyces cerevisiae and its closest relative Saccharomyces paradoxus. The Saccharomyces strains were initially screened for growth on media containing 100 mM glucose and 1.5 mg ml-1 furfural. Five strains were identified that showed a significant tolerance to growth in the presence of furfural and these were then screened for growth and ethanol production in the presence of increasing amounts (0.1-4 mg ml-1) of furfural. Conclusions Of the five furfural tolerant strains S. cerevisiae NCYC 3451 displayed the greatest furfural resistance, and was able to grow in the presence of up to 3.0 mg ml-1 furfural. Furthermore, ethanol production in this strain did not appear to be inhibited by furfural, with the highest ethanol yield observed at 3.0 mg ml-1 furfural. Although furfural resistance was not found to be a trait specific to any one particular lineage or population, three of the strains were isolated from environments where they might be continually exposed to low levels of furfural through the on-going natural degradation of lignocelluloses, and would therefore develop elevated levels of resistance to these furan compounds. Thus these strains represent good candidates for future studies of genetic variation relevant to understanding and manipulating furfural resistance and in the development of tolerant ethanologenic yeast strains for use in bioethanol production from lignocellulose processing

Cell walls of the dimorphic fungal pathogens Sporothrix schenckii and Sporothrix brasiliensis exhibit bilaminate structures and sloughing of extensive and intact layers

This work was supported by the Fundação Carlos Chagas de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), grants E-26/202.974/2015 and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), grants 229755/2013-5, Brazil. LMLB is a senior research fellow of CNPq and Faperj. NG acknowledged support from the Wellcome Trust (Trust (097377, 101873, 200208) and MRC Centre for Medical Mycology (MR/N006364/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Avaliação e tratamento do doente com acne - Parte II: tratamento tópico, sistémico e cirúrgico, tratamento da acne na grávida, algoritmo terapêutico

O Portuguese Acne Advisory Board (PAAB), grupo de dermatologistas portugueses que, à semelhança de grupos congéneres internacionais, tem dedicado particular atenção à definição de linhas de orientação para o tratamento da acne, pretende que o presente documento constitua uma ferramenta útil na abordagem dos doentes com esta patologia. Elaborou-se um dossier, para educação médica contínua, subdividido em 2 partes: Parte I – etiopatogenia e clínica; Parte II – abordagem terapêutica. Nesta Parte II discute-se a abordagem terapêutica – tópica e sistémica – em cada forma clínica de acne, dando particular ênfase aos retinóides e aos antimicrobianos, e salientam-se as estratégias a adoptar para limitar a crescente resistência bacteriana aos antibióticos. Referem-se as indicações específicas para terapêutica hormonal e analisam-se as particularidades do tratamento da acne na grávida e lactante. Descrevem-se algumas técnicas para correcção das cicatrizes da acne. Por último, publica-se um algoritmo que pretende ilustrar a classificação da acne e definir, para cada tipo clínico, a abordagem terapêutica consensualmente recomendada

Avaliação e tratamento do doente com acne – Parte I: Epidemiologia, etiopatogenia, clínica, classificação, impacto psicossocial, mitos e realidades, diagnóstico diferencial e estudos complementares

O Portuguese Acne Advisory Board (PAAB), grupo de dermatologistas portugueses que, à semelhança de grupos congéneres internacionais, tem dedicado particular atenção à definição de linhas de orientação para o tratamento da acne, pretende que o presente documento constitua uma ferramenta útil na abordagem dos doentes com esta patologia. Elaborou-se um dossier, para educação médica contínua, subdividido em 2 partes: Parte I – etiopatogenia e clínica; Parte II – abordagem terapêutica. Nesta Parte I, revêem-se os principais aspectos da clínica e da fisiopatogenia da acne à luz dos conhecimentos actuais. Discute-se a importância do impacto psicológico e social desta entidade e analisam-se os principais mitos e realidades com ela relacionados. Descrevem-se, sucintamente, as patologias mais relevantes no diagnóstico diferencial das lesões de acne. Enumeram-se as indicações para estudo hormonal, bem como os exames a efectuar nos doentes com esta patologia. The Portuguese Acne Advisory Board (PAAB), a group of Portuguese dermatologists with a special interest in acne, develop, as other international groups in this field, consensus recommendations for the treatment of acne. Overall, the goal is to provide a practice guideline to all physicians dealing with this entity. The continuing medical education dossier was divided in two parts: Part I – etiopathogeny and clinical features; Part II – therapy. This Part I reviews acne pathophysiology, clinical aspects, psychological and social impact and several myths surrounding this disease. Some other entities relevant for the differential diagnosis are described. The need of hormonal evaluation is also discusse