OptFlux3: an improved platform for in silico design of cellular factories

The rational design of cellular factories for industrial biotechnology aims to create optimized organisms for the production of bulk chemicals, pharmaceuticals, food ingredients and enzymes, among others. Metabolic engineering (ME) plays a key role in this process, supported by the latest advances in genetic engineering in combination with computational tools to define targets for strain improvement. OptFlux is an open-source reference computational platform for the optimization of cellular factories by the application of in silico ME methods, designed for non-computational experts by providing a user-friendly interface. It allows to load genome-scale models from several sources to be used in the prediction of cellular behavior and identification of metabolic targets for genetic engineering. Its latest version, OptFlux3, allows to perform the simulation of wild type and mutant strains (allowing the simulation of gene/ reaction deletion and over/under expression). Regarding strain optimization, the new architecture opts for a multi-objective framework, allowing users to easily add different goals as optimization targets in a flexible way. Specialized multi-objective algorithms, co-exist with traditional single objectives algorithms to be applied for each case. Also, OptFlux3 includes a new visualization framework for metabolic models and phenotype simulations and a new plug-in management interface that allows to install and remove plug-ins in execution time. Currently available plug-ins include the calculation and visualization of elementary modes, topological analysis and the ability to add reactions/ pathways to existing models. OptFlux is made freely available for all major operating systems, together with suitable documentation in www.optflux.org

Motor coordination, physical activity and fitness as predictors of longitudinal change in adiposity during childhood

The purpose of this study was to examine the influence of motor coordination (MC), physical fitness (PF) and physical activity (PA) on the development of subcutaneous adiposity in a sample of children followed longitudinally from 6 to 10 years of age. Participants were 142 girls and 143 boys. Height, weight, and the triceps and subscapular skinfolds were measured annually between the ages of 6 and 10 years. PA was estimated with the Godin–Shephard questionnaire. MC was evaluated with the Körperkoordination Test für Kinder (KTK) test battery, and PF was assessed with four Fitnessgram tests: curl-ups (CU), push-ups (PU), trunk-lifts (TL) and one mile run/walk (MRW). Hierarchical linear modelling with MC, PF items and PA as predictors of the sum of two skinfolds (SKF) was used. The results showed that boys and girls differed significantly in SKF at baseline (girls: 19.7 mm; boys: 16.6 mm). Three PF items (CU, PU and MRW) and MC had a positive influence on SKF. For each unit improvement in CU, PU, MRW and MC, SKF was reduced by 0.06, 0.04, 0.06 and 0.12 mm, respectively. In conclusion, motor coordination, muscular strength and endurance, and aerobic endurance attenuated the accumulation of subcutaneous adipose tissue during childhood

Lateral Casimir-Polder force with corrugated surfaces

We derive the lateral Casimir-Polder force on a ground state atom on top of a corrugated surface, up to first order in the corrugation amplitude. Our calculation is based on the scattering approach, which takes into account nonspecular reflections and polarization mixing for electromagnetic quantum fluctuations impinging on real materials. We compare our first order exact result with two commonly used approximation methods. We show that the proximity force approximation (large corrugation wavelengths) overestimates the lateral force, while the pairwise summation approach underestimates it due to the non-additivity of dispersion forces. We argue that a frequency shift measurement for the dipolar lateral oscillations of cold atoms could provide a striking demonstration of nontrivial geometrical effects on the quantum vacuum.Comment: 12 pages, 6 figures, contribution to QFEXT07 proceeding

non-linear relationships in children 6-10 years

Background: Given the concern for health?related consequences of an elevated body mass index (BMI; obesity), the potential consequences of a low BMI in children are often overlooked. The purpose was to evaluate the relationship between the BMI across its entire spectrum and motor coordination (MC) in children 6?10 years. Methods: Height, weight, and MC (K?rperkoordinationstest f?r Kinder, KTK test battery) were measured in 1,912 boys and 1,826 girls of 6?10 years of age. BMI (kg/m2) was calculated. KTK scores for each of the four tests were also converted to a motor quotient (MQ). One?way ANOVA was used to test differences in the BMI, individual test items, and MQ among boys and girls within age groups. Sex?specific quadratic regressions of individual KTK items and the MQ on the BMI were calculated. Girls and boys were also classified into four weight status groups using International Obesity Task Force criteria: thin, normal, overweight, and obese. Differences in specific test items and MQ between weight status groups were evaluated by age group in each sex. Results: Thirty?one percent of the sample was overweight or obese, whereas 5% was thin. On average, normal weight children had the highest MQ in both sexes across the age range with few exceptions. Overweight/obese children had a lower MQ than normal weight and thin children. The quadratic regression lines generally presented an inverted parabolic relationship between the BMI and MC and suggested a decrease in MC with an increase in the BMI. Conclusion: In general, BMI shows a curvilinear, inverted parabolic relationship with MC in children 6?10 years.4811-99FE-2ECD | Luis Paulo Rodriguesinfo:eu-repo/semantics/publishedVersio

Evaluating simulated annealing algorithms in the optimization of bacterial strains

In this work, a Simulated Annealing (SA) algorithm is proposed for a Metabolic Engineering task: the optimization of the set of gene deletions to apply to a microbial strain to achieve a desired production goal. Each mutant strain is evaluated by simulating its phenotype using the Flux-Balance Analysis approach, under the premise that microorganisms have maximized their growth along natural evolution. A set based representation is used in the SA to encode variable sized solutions, enabling the automatic discovery of the ideal number of gene deletions. The approach was compared to the use of Evolutionary Algorithms (EAs) to solve the same task. Two case studies are presented considering the production of succinic and lactic acid as the target, with the bacterium E. coli. The variable sized SA seems to be the best alternative, outperforming the EAs, showing a fast convergence and low variability among the several runs and also enabing the automatic discovery of the ideal number of knockouts.FEDER.Portuguese Foundation for Science and Technology (FCT) - POSC/EIA/59899/2004

Casimir torque between corrugated metallic plates

We consider two parallel corrugated plates and show that a Casimir torque arises when the corrugation directions are not aligned. We follow the scattering approach and calculate the Casimir energy up to second order in the corrugation amplitudes, taking into account nonspecular reflections, polarization mixing and the finite conductivity of the metals. We compare our results with the proximity force approximation, which overestimates the torque by a factor 2 when taking the conditions that optimize the effect. We argue that the Casimir torque could be measured for separation distances as large as 1 $\mu{\rm m}.$Comment: 7 pages, 3 figures, contribution to QFEXT07 proceeding

Correlation between BMI and motor coordination in children

Objectives: To analyze the association between motor coordination (MC) and body mass index (BMI) across childhood and early adolescence. Design: This study is cross-sectional. Methods: Data were collected in 7175 children (boys n = 3616, girls n = 3559), ages 6–14 years. BMI was calculated from measured height and weight [body mass (kg)/height (m2)]. Motor coordination was evaluated using Kiphard-Schilling’s body coordination test (KTK). Spearman’s rank correlation was used to study the association between BMI and MC. A Kruskal–Wallis test was used to analyze the differences in MC between children of normal weight, overweight and obese children. Results: Correlations between MC and BMI were negative and varied between 0.05 and 0.49. The highest negative correlations for both boys and girls was at 11 years of age. There was a general pattern of increasing negative correlations in both genders from 6 to 11 years of age and then a decrease in correlation strengths through 14 years of age. In both boys (χ2 (2) = 324.01; p < 0.001) and girls (χ2 (2) = 291.20; p < 0.001) there were significant differences in MC between the three groups’ weight status. Normal weight children of both sexes demonstrated significantly higher MC scores than overweight. Obese children in both sexes had the lowest MC scores among all three groups. Conclusion: Motor coordination demonstrated an inverse relationship with BMI across childhood and into early adolescence. The strength of the inverse relation increased during childhood, but decreased through early adolescence. Overweight and obese children of both sexes demonstrated significantly lower MC than normal weight children

Decoherence via Dynamical Casimir Effect

We derive a master equation for a mirror interacting with the vacuum field via radiation pressure. The dynamical Casimir effect leads to decoherence of a 'Schroedinger cat' state in a time scale that depends on the degree of 'macroscopicity' of the state components, and which may be much shorter than the relaxation time scale. Coherent states are selected by the interaction as pointer states.Comment: 4 pages, 2 figure

A coordenação motora é preditora dos níveis de actividade física habitual?

Os níveis de actividade física habitual (AF) são um factor importante na prevenção de uma série de doenças crónicas. Supõe-se que os hábitos de AF que se instalam durante a infância poderão perdurar até à idade adulta, contudo não estão esclarecidos quais os factores associados à adesão à prática de AF. O objectivo deste trabalho é estudar a associação dos níveis de AF com a coordenação motora (CM), as habilidades motoras (HM) e a aptidão física (ApF) em crianças. A amostra foi constituída por 144 crianças (meninas n = 68, meninos n = 78) com idades compreendidas entre os 4 e os 9 anos. Foi utilizada bateria Fitnessgram para avaliar a ApF nos seguintes itens (apenas nas crianças com idade superior a 5 anos: push-up, curl-up, trunk-lift e corrida/marcha da milha. A coordenação motora foi avaliação através da bateria KTK. As habilidades motoras foram avaliadas com a bateria TGMD2. A AF habitual foi avaliada através de pedometria, tendo sido colocado em cada criança um pedómetro que recolheu os passos ao longo de uma semana completa. Para análise foi considerada a média diária de passos. Foi realizada uma regressão múltipla passo-a-passo, tendo a AF como variável dependente. De todas as variáveis apenas a avaliação locomotora da bateria de habilidades motoras TGMD2 foi retida como preditor dos níveis de AF. A variância explicada é baixa (1%)