Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Relationship between oviposition preference and offspring performance in Australian Helicoverpa armigera (Hubner) (Lepidoptera : Noctuidae)

We investigated the oviposition preference and larval performance of Helicoverpa armigera under laboratory conditions to determine if the oviposition preference of individual females on maize, cowpea and cotton correlates with offspring performance on the leaves of the same host plants. The host-plant preference hierarchy of females did not correlate with their offspring performance. Female moths chose host plants that contributed less to their offspring fitness. Plant effects accounted for the largest amount of variation in offspring performance, while the effects of female (family) was low. The offspring of most females (80%, n = 10) were broadly similar, but 20% (two out of 10), showed marked difference in their offspring performance across the host-plant species. Similarly, there was no relation between larval feeding preference and performance. However, like most laboratory experiments, our experi-mental design does not allow the evaluation of ecological factors (for example, natural enemies, host abundance, etc.) that can play an important role in larval performance in the field. Overall, the results highlight the importance of carrying out preference performance analysis on the individual or family level, rather than pooling individuals to obtain average population data.

Mean anisotropy of homogeneous Gaussian random fields and anisotropic norms of linear translation-invariant operators on multidimensional integer lattices

Sensitivity of output of a linear operator to its input can be quantified in various ways. In Control Theory, the input is usually interpreted as disturbance and the output is to be minimized in some sense. In stochastic worst-case design settings, the disturbance is considered random with imprecisely known probability distribution. The prior set of probability measures can be chosen so as to quantify how far the disturbance deviates from the white-noise hypothesis of Linear Quadratic Gaussian control. Such deviation can be measured by the minimal Kullback-Leibler informational divergence from the Gaussian distributions with zero mean and scalar covariance matrices. The resulting anisotropy functional is defined for finite power random vectors. Originally, anisotropy was introduced for directionally generic random vectors as the relative entropy of the normalized vector with respect to the uniform distribution on the unit sphere. The associated a-anisotropic norm of a matrix is then its maximum root mean square or average energy gain with respect to finite power or directionally generic inputs whose anisotropy is bounded above by a≥0. We give a systematic comparison of the anisotropy functionals and the associated norms. These are considered for unboundedly growing fragments of homogeneous Gaussian random fields on multidimensional integer lattice to yield mean anisotropy. Correspondingly, the anisotropic norms of finite matrices are extended to bounded linear translation invariant operators over such fields.

Rock fracture mean trace length estimation and confidence interval calculation using maximum likelihood methods

There has been a resurgence of interest in the mean trace length estimator of Pahl for window sampling of traces. The estimator has been dealt with by Mauldon and Zhang and Einstein in recent publications. The estimator is a very useful one in that it is non-parametric. However, despite some discussion regarding the statistical distribution of the estimator, none of the recent works or the original work by Pahl provide a rigorous basis for the determination a confidence interval for the estimator or a confidence region for the estimator and the corresponding estimator of trace spatial intensity in the sampling window. This paper shows, by consideration of a simplified version of the problem but without loss of generality, that the estimator is in fact the maximum likelihood estimator (MLE) and that it can be considered essentially unbiased. As the MLE, it possesses the least variance of all estimators and confidence intervals or regions should therefore be available through application of classical ML theory. It is shown that valid confidence intervals can in fact be determined. The results of the work and the calculations of the confidence intervals are illustrated by example. (C) 2003 Elsevier Science Ltd. All rights reserved.

Capillary bridging and long-range attractive forces in a mean-field approach

When a mixture is confined, one of the phases can condense out. This condensate, which is otherwise metastable in the bulk, is stabilized by the presence of surfaces. In a sphere-plane geometry, routinely used in atomic force microscope and surface force apparatus, it, can form a bridge connecting the surfaces. The pressure drop in the bridge gives rise to additional long-range attractive forces between them. By minimizing the free energy of a binary mixture we obtain the force-distance curves as well as the structural phase diagram of the configuration with the bridge. Numerical results predict a discontinuous transition between the states with and without the bridge and linear force-distance curves with hysteresis. We also show that similar phenomenon can be observed in a number of different systems, e.g., liquid crystals and polymer mixtures. (C). 2004 American Institute of Physics.

The effect of long-chain polyunsaturated fatty acids intake during pregnancy on adiposity of healthy full-term offspring at birth

Objective - The adjusted effect of long-chain polyunsaturated fatty acid (LCPUFA) intake during pregnancy on adiposity at birth of healthy full-term appropriate-for-gestational age neonates was evaluated. Study Design - In a cross-sectional convenience sample of 100 mother and infant dyads, LCPUFA intake during pregnancy was assessed by food frequency questionnaire with nutrient intake calculated using Food Processor Plus. Linear regression models for neonatal body composition measurements, assessed by air displacement plethysmography and anthropometry, were adjusted for maternal LCPUFA intakes, energy and macronutrient intakes, prepregnancy body mass index and gestational weight gain. Result - Positive associations between maternal docosahexaenoic acid intake and ponderal index in male offspring (β=0.165; 95% confidence interval (CI): 0.031–0.299; P=0.017), and between n-6:n-3 LCPUFA ratio intake and fat mass (β=0.021; 95% CI: 0.002–0.041; P=0.034) and percentage of fat mass (β=0.636; 95% CI: 0.125–1.147; P=0.016) in female offspring were found. Conclusion - Using a reliable validated method to assess body composition, adjusted positive associations between maternal docosahexaenoic acid intake and birth size in male offspring and between n-6:n-3 LCPUFA ratio intake and adiposity in female offspring were found, suggesting that maternal LCPUFA intake strongly influences fetal body composition.

Pregnancy rates and predictors in women with HIV/AIDS in Rio de Janeiro, Southeastern Brazil

OBJECTIVE: To assess incidence and predictors of first pregnancy among women with HIV/AIDS. METHODS: Prospective cohort study was conducted in Rio de Janeiro, southeastern Brazil, between 1996 and 2003. This study comprised 225 women with HIV/AIDS followed up until their first pregnancy or first censored event (hysterectomy, tubal ligation, menopause, 50 years of age, loss to follow-up, death or the end of December 2003). Pregnancy and abortion rates were estimated, and Cox proportional hazards models were used to identify baseline characteristics associated with pregnancy risk. RESULTS: The women were followed up for 565 person/years with a median follow-up of 3 years per women. The mean age was 32 years (SD: 7), and 54.7% were white. There were 60 pregnancies in 39 women, and 18 were terminated (induced abortions), accounting for a rate of 6.9% and 2.1% women/year, respectively. Repeated pregnancies occurred in 33.3% of the women (13/39). Higher pregnancy risk was seen among younger women (HR=3.42; 95%CI: 1.69;6.95) and those living with their partners (HR=1.89; 95%CI: 1.00;3.57). Lower pregnancy risk was associated with higher education level (HR=0.43; 95%CI: 0.19;0.99) and use of antiretroviral therapy (HR=061; 95%CI: 0.31;1.17). CONCLUSIONS: Lower pregnancy rates were found in our cohort than in the general population. Sociodemographic characteristics should be taken into consideration in the management of reproductive health in HIV-positive childbearing age women. Reproductive and family planning counseling must be incorporated into HIV/AIDS programs for women to help preventing HIV transmission to their partners and offspring.

Approximating fractional derivatives through the generalized mean

This paper addresses the calculation of fractional order expressions through rational fractions. The article starts by analyzing the techniques adopted in the continuous to discrete time conversion. The problem is re-evaluated in an optimization perspective by tacking advantage of the degree of freedom provided by the generalized mean formula. The results demonstrate the superior performance of the new algorithm.

Electric vehicles as a mean to reduce, energy, emissions and electricity costs

Electric vehicles (EVs) and plug-in hybrid electric vehicles (PHEVs), which obtain their fuel from the grid by charging a battery, are set to be introduced into the mass market and expected to contribute to oil consumption reduction. This research is concerned with studying the potential impacts on the electric utilities of large-scale adoption of plug-in electric vehicles from the perspective of electricity demand, fossil fuels use, CO2 emissions and energy costs. Simulations were applied to the Portuguese case study in order to analyze what would be the optimal recharge profile and EV penetration in an energy-oriented, an emissions-oriented and a cost-oriented objective. The objectives considered were: The leveling of load profiles, minimization of daily emissions and minimization of daily wholesale costs. Almost all solutions point to an off-peak recharge and a 50% reduction in daily wholesale costs can be verified from a peak recharge scenario to an off-peak recharge for a 2 million EVs in 2020. A 15% improvement in the daily total wholesale costs can be verified in the costs minimization objective when compared with the off-peak scenario result.

The electric vehicles as a mean to reduce Co2 emissions and energy costs in isolated regions: the São Miguel (Azores) case study

Most of small islands around the world today, are dependent on imported fossil fuels for the majority of their energy needs especially for transport activities and electricity production. The use of locally renewable energy resources and the implementation of energy efficiency measures could make a significant contribution to their economic development by reducing fossil fuel imports. An electrification of vehicles has been suggested as a way to both reduce pollutant emissions and increase security of supply of the transportation sector by reducing the dependence on oil products imports and facilitate the accommodation of renewable electricity generation, such as wind and, in the case of volcanic islands like Sao Miguel (Azores) of the geothermal energy whose penetration has been limited by the valley electricity consumption level. In this research, three scenarios of EV penetration were studied and it was verified that, for a 15% LD fleet replacement by EVs with 90% of all energy needs occurring during the night, the accommodation of 10 MW of new geothermal capacity becomes viable. Under this scenario, reductions of 8% in electricity costs, 14% in energy, 23% in fossil fuels use and CO2 emissions for the transportation and electricity production sectors could be expected.

The Effect of Long-Chain Polyunsaturated Fatty Acids Intake During Pregnancy on Adiposity of Healthy Full-Term Offspring at Birth

OBJECTIVE: The adjusted effect of long-chain polyunsaturated fatty acid (LCPUFA) intake during pregnancy on adiposity at birth of healthy full-term appropriate-for-gestational age neonates was evaluated. STUDY DESIGN: In a cross-sectional convenience sample of 100 mother and infant dyads, LCPUFA intake during pregnancy was assessed by food frequency questionnaire with nutrient intake calculated using Food Processor Plus. Linear regression models for neonatal body composition measurements, assessed by air displacement plethysmography and anthropometry, were adjusted for maternal LCPUFA intakes, energy and macronutrient intakes, prepregnancy body mass index and gestational weight gain. RESULT: Positive associations between maternal docosahexaenoic acid intake and ponderal index in male offspring (β=0.165; 95% confidence interval (CI): 0.031-0.299; P=0.017), and between n-6:n-3 LCPUFA ratio intake and fat mass (β=0.021; 95% CI: 0.002-0.041; P=0.034) and percentage of fat mass (β=0.636; 95% CI: 0.125-1.147; P=0.016) in female offspring were found. CONCLUSION: Using a reliable validated method to assess body composition, adjusted positive associations between maternal docosahexaenoic acid intake and birth size in male offspring and between n-6:n-3 LCPUFA ratio intake and adiposity in female offspring were found, suggesting that maternal LCPUFA intake strongly influences fetal body composition.