Non-singular inflation with vacuum decay

On the basis of a semi-classical analysis of vacuum energy in an expanding spacetime, we describe a non-singular cosmological model in which the vacuum density decays with time, with a concomitant production of matter. During an infinitely long period we have an empty, inflationary universe, with H \approx 1. This primordial era ends in a fast phase transition, during which H and \Lambda decrease to nearly zero in a few Planck times, with release of a huge amount of radiation. The late-time scenario is similar to the standard model, with the radiation phase followed by a long dust era, which tends asymptotically to a de Sitter universe, with vacuum dominating again. An analysis of the redshift-distance relation for supernovas Ia leads to cosmological parameters in agreement with other current estimations.Comment: Work presented at IRGAC 2006, Barcelona, July 11-15 2006. To appear in a special issue of Journal of Physics

Fermi liquid theory of electronic topological transitions and screening anomalies in metals

General expressions for the contributions of the Van Hove singularity (VHS)in the electron density of states to the thermodynamic potential $\Omega are obtained in the framework of microscopic Fermi liquid theory. The renormalization of the singularities in$\Omega connected with the Lifshitz electronic topological transition (ETT) is found. Screening anomalies due to virtual transitions between VHS and the Fermi level are considered. It is shown that, in contrast with the one-particle picture of ETT, the singularities in $\Omega turns out to be two-sided for interacting electrons.Comment: 8 pages RevTeX, with minor corrections (Introduction and Conclusions are rewritten, new references are added), to appear in Physical review

Footprinting microbial metabolites in nature and medicine

The study of metabolic alterations in response to genetic and environmental perturbations has been a central topic in microbial metabolomics (Fiehn, 2002; Kol et al., 2010; Villas-Boas et al., 2008). Some of these alterations can be readily detected by changes in their surroundings, normally associated with metabolites that are released by cells as by-products of the metabolism or as extracellular signalling molecules to mediate cross-talk within microbial communities. The analysis of these metabolites, also known as metabolic footprinting, has been widely applied with different purposes: discriminating between metabolic phenotypes in order to classify and identify mutant strains (Villas-Boas et al., 2008); monitoring bioprocesses with the aim to detect specific metabolites that indicate alterations in the culture performance (Carneiro et al., 2011; Sue et al., 2011); and identifying quorum-sensing metabolites that indicate potential targets to annihilate pathogens (Birkenstock et al., 2012). These metabolic readouts have been also useful to give insights into intracellular metabolic activities and provide a straightforward way to analyse simultaneously multiple metabolic activities, since no extraction procedures are required to analyse the endometabolome (i.e., intracellular metabolites). Thus, through metabolic footprint analysis we can assess central metabolic activities that characterize the reproduction and survival of organisms. We have developed a methodology to evaluate the metabolic state of microbial cultures by analysing the footprints of two microbial systems: the bacterium Escherichia coli and the human pathogen Helicobacter pylori. Strategies for sampling and sample preparation were developed, as well as the analytical procedures based on gas chromatography with mass spectrometry (GC-MS). A wide variety of metabolites was detected, including fatty, amino and organic acids, which allowed us to address changes in most central metabolic pathways, such as the tricarboxylic acid cycle (TCA cycle), the biosynthesis of amino and fatty acids, as well as other energy generating metabolic reactions. The analysis of extracellular metabolites of E. coli cultures at different growth conditions were first performed to discriminate the physiological state of cultures and to evaluate the metabolic alterations produced at different growth conditions. According to our results in these experiments, metabolic footprints are good indicators of alterations in the intracellular metabolism. Next, the metabolic footprints of H. pylori cultures were investigated to get insights on the catabolism of this human pathogen. Overall, fifteen amino acids were detected in extracellular medium; six of them were confirmed as essentials for H. pylori growth, four amino acids were identified as non-essentials and can be used as carbon source, whilst five amino acids were identified as non-essentials and non-carbon source. In addition, some organic acids were also identified as carbon sources for H. pylori. This metabolic footprint analysis of H. pylori cultures allowed us to uncover key metabolic activities, mainly related with amino acids catabolism and to get insight on the metabolic behaviour of this organism. The characterization of catabolic pathways, as well as of possible metabolic constraints, is of major importance to understand the dynamic basis of the interactions host–microbe in the human gut, and in particular to discover potential ‘diagnostic’ biomarkers. It is well-known that pathogen's metabolism can influence the host health and may affect drug metabolism, toxicity and the efficacy of therapies (Holmes et al., 2011). However, little is known about their metabolic structure and behaviour. Our methodology allows uncovering part of the metabolic structure of H. pylori metabolism and undisclosed catabolic activities. Acknowledgments This work was partially supported by the MIT-Portugal Program in Bioengineering (MIT-Pt/BS-BB/0082/2008), the research project HeliSysBio-Molecular Systems Biology Helicobacter pylori (FCT PTDC/EBB-EBI/104235/2008) and a Post-doc grant from Portuguese FCT (Fundação para a Ciência e Tecnologia) (ref. SFRH/BPD/73951/2010). 1. Fiehn O. 2002. Metabolomics - the link between genotypes and phenotypes. Plant Molecular Biology 48: 155-71. 2. Kol S, Merlo ME, Scheltema RA, de VM, Vonk RJ, Kikkert NA, Dijkhuizen L, Breitling R, Takano E. 2010. Metabolomic characterization of the salt stress response in Streptomyces coelicolor. Applied and Environmental Microbiology 76: 2574-81. 3. Villas-Boas SG, Moon CD, Noel S, Hussein H, Kelly WJ, Cao M, Lane GA, Cookson AL, Attwood GT. 2008. Phenotypic characterization of transposon-inserted mutants of Clostridium proteoclasticum B316(T) using extracellular metabolomics. Journal of Biotechnology 134: 55-63. 4. Sue T, Obolonkin V, Griffiths H, Villas-Boas SG. 2011. An exometabolomics approach to monitoring microbial contamination in microalgal fermentation processes by using metabolic footprint analysis. Appl Environ Microbiol 77: 7605-10. 5. Carneiro S, Villas-Boas SG, Ferreira EC, Rocha I. 2011. Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations. Molecular Biosystems 7: 899-910. 6. Birkenstock T, Liebeke M, Winstel V, Krismer B, Gekeler C, Niemiec MJ, Bisswanger H, Lalk M, Peschel A. 2012. Exometabolome analysis identifies pyruvate dehydrogenase as a target for the antibiotic triphenylbismuthdichloride in multiresistant bacterial pathogens. J Biol Chem 287: 2887-95. 7. Holmes E, Li JV, Athanasiou T, Ashrafian H, Nicholson JK. 2011. Understanding the role of gut microbiome-host metabolic signal disruption in health and disease. Trends Microbiol 19: 349-59

Entanglement in coined quantum walks on regular graphs

Published versio

Scaffolding MATLAB and octave software comprehension through visualization

Multiple view interactive environments (MVIEs) provide visual resources to support the comprehension of a specific domain dataset. For any domain, different views can be selected and configured in a real time fashion to be better adjusted to the user needs. This paper focuses on the use of a MVIE called OctMiner to support the comprehension of MATLAB and GNU/Octave programs. The authors conducted a case study to characterize the use of OctMiner in the context of comprehension activities. Results provide preliminary evidence of the effectiveness of OctMiner to support the comprehension of programs written in MATLAB and Octave.info:eu-repo/semantics/acceptedVersio

A multiple view interactive environment to support MATLAB and GNU/Octave program comprehension

Program comprehension plays an important role in Software Engineering. In fact, many of the software lifecycle activities depend on program comprehension. Despite the importance of MATLAB and Octave programing languages in the Engineering and Statistical communities, little attention has been paid to the conception, implementation and characterization of tools and techniques for the comprehension of programs written in these languages. Considering this scenario, this paper presents a Multiple View Interactive Environment (MVIE) called OctMiner that supports the comprehension of programs developed in the aforementioned languages. OctMiner provides a set of coordinated visual metaphors that can be adjusted in accordance with the comprehension goals. An example is presented to illustrate the main functionalities of OctMiner in a real scenario of program comprehension.info:eu-repo/semantics/acceptedVersio

On the use of a multiple view interactive environment for MATLAB and octave program comprehension

WOS:000364988500049 (Nº de Acesso Web of Science)MATLAB or GNU/Octave programs can become very large and complex and therefore difficult to understand and maintain. The objective of this paper is presenting an approach to mitigate this problem, based upon a multiple view interactive environment (MVIE) called OctMiner. The latter provides visual resources to support program comprehension, namely the selection and configuration of several views to meet developers’ needs. For validation purposes, the authors conducted two case studies to characterize the use of OctMiner in the context of software comprehension activities. The results provided initial evidences of its effectiveness to support the comprehension of programs written in the aforementioned languages

Sugars metabolism and ethanol production by different yeast strains from coffee industry wastes hydrolysates

Significant amounts of wastes are generated by the coffee industry, among of which, coffee silverskin (CS) and spent coffee grounds (SCG) are the most abundantly generated during the beans roasting and instant coffee preparation, respectively. This study evaluated the sugars metabolism and production of ethanol by three different yeast strains (Saccharomyces cerevisiae, Pichia stipitis and Kluyveromyces fragilis) when cultivated in sugar rich hydrolysates produced by acid hydrolysis of CS and SCG. S. cerevisiae provided the best ethanol production from SCG hydrolysate (11.7 g/l, 50.2% efficiency). On the other hand, insignificant (⩽1.0 g/l) ethanol production was obtained from CS hydrolysate, for all the evaluated yeast strains, probably due to the low sugars concentration present in this medium (approx. 22 g/l). It was concluded that it is possible to reuse SCG as raw material for ethanol production, which is of great interest for the production of this biofuel, as well as to add value to this agro-industrial waste. CS hydrolysate, in the way that is produced, was not a suitable fermentation medium for ethanol production; however, the hydrolysate concentration for the sugars content increase previous the use as fermentation medium could be an alternative to overcome this problem

Estádio mais adequado de manejo do milheto para fins de adubação verde.

O milheto [Pennisetum glaucum (L.) R. Brown] é uma opção importante dentre as espécies vegetais para adubação verde. É uma planta anual, forrageira de verão, de clima tropical, hábito ereto, porte alto, e pode atingir até 5 m de altura. Dentre as principais características do milheto ressaltam-se: tolerância à seca, capacidade em adaptar-se a diferentes solos, facilidade de produzir sementes e boa adaptação à mecanização. Essa espécie vem sendo utilizada com maior intensidade, no Cerrado, no período de safrinha (fevereiro a abril) e na primavera (agosto a outubro), como adubo verde e cobertura do solo para plantio direto e outras finalidades, por exemplo, na integração lavoura-pecuária (BURLE et al., 2006).bitstream/item/51825/1/COT-2011-171.pd