Directionality principles in thermodynamics and evolution

Directionality in populations of replicating organisms can be parametrized in terms of a statistical concept: evolutionary entropy. This parameter, a measure of the variability in the age of reproducing individuals in a population, is isometric with the macroscopic variable body size. Evolutionary trends in entropy due to mutation and natural selection fall into patterns modulated by ecological and demographic constraints, which are delineated as follows: (i) density-dependent conditions (a unidirectional increase in evolutionary entropy), and (ii) density-independent conditions, (a) slow exponential growth (an increase in entropy); (b) rapid exponential growth, low degree of iteroparity (a decrease in entropy); and (c) rapid exponential growth, high degree of iteroparity (random, nondirectional change in entropy). Directionality in aggregates of inanimate matter can be parametrized in terms of the statistical concept, thermodynamic entropy, a measure of disorder. Directional trends in entropy in aggregates of matter fall into patterns determined by the nature of the adiabatic constraints, which are characterized as follows: (i) irreversible processes (an increase in thermodynamic entropy) and (ii) reversible processes (a constant value for entropy). This article analyzes the relation between the concepts that underlie the directionality principles in evolutionary biology and physical systems. For models of cellular populations, an analytic relation is derived between generation time, the average length of the cell cycle, and temperature. This correspondence between generation time, an evolutionary parameter, and temperature, a thermodynamic variable, is exploited to show that the increase in evolutionary entropy that characterizes population processes under density-dependent conditions represents a nonequilibrium analogue of the second law of thermodynamics.

Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution.

The internal transcribed spacers (ITS) of nuclear ribosomal DNA of 33 species of genus Paeonia (Paeoniaceae) were sequenced. In section Paeonia, different patterns of nucleotide additivity were detected in 14 diploid and tetraploid species at sites that are variable in the other 12 species of the section, suggesting that reticulate evolution has occurred. Phylogenetic relationships of species that do not show additivity, and thus ostensibly were not derived through hybridization, were reconstructed by parsimony analysis. The taxa presumably derived through reticulate evolution were then added to the phylogenetic tree according to additivity from putative parents. The study provides an example of successfully using ITS sequences to reconstruct reticulate evolution in plants and further demonstrates that the sequence data could be highly informative and accurate for detecting hybridization. Maintenance of parental sequences in the species of hybrid origin is likely due to slowing of concerted evolution caused by the long generation time of peonies. The partial and uneven homogenization of parental sequences displayed in nine species of putative hybrid origin may have resulted from gradients of gene conversion. The documented hybridizations may have occurred since the Pleistocene glaciations. The species of hybrid origin and their putative parents are now distantly allopatric. Reconstruction of reticulate evolution with sequence data, therefore, provides gene records for distributional histories of some of the parental species.

Sociality and the rate of molecular evolution

The molecular clock does not tick at a uniform rate in all taxa but maybe influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonsocial relatives because of greatly reduced effective population size; if most individuals in a population are nonreproductive and only one or few queens produce all the offspring, then eusocial animals could have much lower effective population sizes than their solitary relatives, which should increase the rate of substitution of nearly neutral mutations. An earlier study reported faster rates in eusocial honeybees and vespid wasps but failed to correct for phylogenetic nonindependence or to distinguish between potential causes of rate variation. Because sociality has evolved independently in many different lineages, it is possible to conduct a more wide-ranging study to test the generality of the relationship. We have conducted a comparative analysis of 25 phylogenetically independent pairs of social lineages and their nonsocial relatives, including bees, wasps, ants, termites, shrimps, and mole rats, using a range of available DNA sequences (mitochondrial and nuclear DNA coding for proteins and RNAs, and nontranslated sequences). By including a wide range of social taxa, we were able to test whether there is a general influence of sociality on rates of molecular evolution and to test specific predictions of the hypothesis: (1) that social species have faster rates because they have reduced effective population sizes; (2) that mitochondrial genes would show a greater effect of sociality than nuclear genes; and (3) that rates of molecular evolution should be correlated with the degree of sociality. We find no consistent pattern in rates of molecular evolution between social and nonsocial lineages and no evidence that mitochondrial genes show faster rates in social taxa. However, we show that the most highly eusocial Hymenoptera do have faster rates than their nonsocial relatives. We also find that social parasites (that utilize the workers from related species to produce their own offspring) have faster rates than their social relatives, which is consistent with an effect of lower effective population size on rate of molecular evolution. Our results illustrate the importance of allowing for phylogenetic nonindependence when conducting investigations of determinants of variation in rate of molecular evolution.

Phylogenetic analysis of within -host serially-sampled viral data

The primary goal of this dissertation is the study of patterns of viral evolution inferred from serially-sampled sequence data, i.e., sequence data obtained from strains isolated at consecutive time points from a single patient or host. RNA viral populations have an extremely high genetic variability, largely due to their astronomical population sizes within host systems, high replication rate, and short generation time. It is this aspect of their evolution that demands special attention and a different approach when studying the evolutionary relationships of serially-sampled sequence data. New methods that analyze serially-sampled data were developed shortly after a groundbreaking HIV-1 study of several patients from which viruses were isolated at recurring intervals over a period of 10 or more years. These methods assume a tree-like evolutionary model, while many RNA viruses have the capacity to exchange genetic material with one another using a process called recombination. ^ A genealogy involving recombination is best described by a network structure. A more general approach was implemented in a new computational tool, Sliding MinPD, one that is mindful of the sampling times of the input sequences and that reconstructs the viral evolutionary relationships in the form of a network structure with implicit representations of recombination events. The underlying network organization reveals unique patterns of viral evolution and could help explain the emergence of disease-associated mutants and drug-resistant strains, with implications for patient prognosis and treatment strategies. In order to comprehensively test the developed methods and to carry out comparison studies with other methods, synthetic data sets are critical. Therefore, appropriate sequence generators were also developed to simulate the evolution of serially-sampled recombinant viruses, new and more through evaluation criteria for recombination detection methods were established, and three major comparison studies were performed. The newly developed tools were also applied to "real" HIV-1 sequence data and it was shown that the results represented within an evolutionary network structure can be interpreted in biologically meaningful ways. ^

Shift Scheduling in Services When Employees Have Limited Availability: An L. P. Approach

This paper compares two linear programming (LP) models for shift scheduling in services where homogeneously-skilled employees are available at limited times. Although both models are based on set covering approaches, one explicitly matches employees to shifts, while the other imposes this matching implicitly. Each model is used in three forms—one with complete, another with very limited meal break placement flexibility, and a third without meal breaks—to provide initial schedules to a completion/improvement heuristic. The term completion/improvement heuristic is used to describe a construction/ improvement heuristic operating on a starting schedule. On 80 test problems varying widely in scheduling flexibility, employee staffing requirements, and employee availability characteristics, all six LP-based procedures generated lower cost schedules than a comparison from-scratch construction/improvement heuristic. This heuristic, which perpetually maintains an explicit matching of employees to shifts, consists of three phases which add, drop, and modify shifts. In terms of schedule cost, schedule generation time, and model size, the procedures based on the implicit model performed better, as a group, than those based on the explicit model. The LP model with complete break placement flexibility and implicitly matching employees to shifts generated schedules costing 6.7% less than those developed by the from-scratch heuristic.

Produção de carboidratos a partir do efluente de laticínios tratado por cianobactéria

Nesta tese foi demonstrado o potencial de produção de carboidratos por Aphanothece microscopica Nägeli cultivada no efluente oriundo de uma indústria de laticínios. Para tanto, o trabalho é composto de quatro artigos que objetivaram avaliar a produção de carboidratos em função da temperatura, inóculo e razões C/N e N/P do elfluente, bem como a possibilidade de reúso da água residuária. Foram utilizadas temperaturas de (10, 20 e 30ºC) e inóculo (100, 200 e 300 mg.L-1). A melhor condição indicada foi quando utilizou-se a temperatura de 30°C e 200 mg.L-1 de inóculo. Na sequência, considerando a temperatura e a concentração celular selecionada, foi estudada a influência das razões C/N e N/P na produção de carboidratos. Para tal, C/N (20, 40 e 60) e N/P (5, 10 e 15) na produção de carboidratos extracelulares foram avaliadas em cultivos a 30°C, tendo como inóculo 200 mg.L-1. Os melhores resultados obtidos, foram quando foi utilizado C/N 60 e N/P 10. Uma vez definidas as melhores condições de produção de carboidratos, foi estudado o processo de separação de biomassa do meio de cultivo, a partir dos coagulantes FeCl3, Al2(SO4)3 e tanino. O efeito dos coagulantes na separação da biomassa foram estudados, quanto ao pH (6,0, 7,0 e 8,0) e concentração de coagulantes (50, 300 e 550 mg.L-1), utilizando como parâmetro de medida, a eficiência de remoção de DQO, turbidez e sólidos suspensos (SS). Os resultados demonstraram que as concentrações de coagulantes influenciaram significativamente ao nível de significância de 5 %, na separação da biomassa, com eficiência significativa na remoção da DQO, turbidez e SS. A melhor condição avaliada foi a que utilizou tanino na concentração de 300 mg.L-1 e pH 7,0, o que resultou em uma água residuária com remoção média de 96 % da turbidez, com potencial de ser reutilizada. Por fim, foi realizada a identificação de carboidratos gerados por Aphanothece microscopica Nägeli. Os resultados evidenciaram uma biomassa com até 33,5 % de carboidratos totais, perfazendo uma fração de carboidratos extracelulares, na fase estacionária de crescimento celular, de aproximadamente 25 % e 8 % os carboidratos da parede celular. Ficou demonstrado ainda que a composição dos carboidratos extracelulares do microorganismo em estudo é constituído por mono e dissacarídeos perfazendo concentrações na ordem de 12,88 % de glicose, 3,54 % de rafinose, 3,43 % sacarose, 2,13 % de frutose e 2,45 % de ribose. Ficou demonstrado o potencial de produção de carboidratos por Aphanothece microscopica Nägeli quando cultivada no efluente da indústria de laticínios.

Can gut microbiota analysis be beneficial for ex-situ and in-situ conservation of threatened animal species?

Ex-situ conservation and the in-situ conservation of natural habitats are the tools to conserve biodiversity. Habitats and ecosystems have been becoming altered by human activities and a growing number of species requires form of management to ensure their survival. Conservation queries become more complex and urgent. Developing scientifically based and innovative approaches to ex-situ conservation is necessary. Recent studies underline importance of gut microbiome in animal health with implications for animal conservation and management. Animal and human studies have demonstrated that environmental factors can impact gut microbiome composition. Within this scenario, the present work focused on species belonging to different taxa, reptiles and mammals: Aldabrachelys gigantea, the giant tortoise of the Seychelles islands and Indri indri, the greatest leaving lemur of Madagascar. The Seychelles giant tortoise is vulnerable species with declining population, whereas the indri is a critically endangered species that could reach the extinction within 25 years. Both need research to help them to survive. Tortoises live for very long time and to observe how they can afford the environmental changes is very difficult. Indris, instead, are able to survive only in a small area of the Madagascar forest, with a very strong link between the species’ survival and the environment. The obtained results underline importance of environmental factors, both in-situ and ex-situ, for species conservation. Microbiome could help the organisms to respond on a short timescale and cope with, environmental changes. However, species with long generation time might not be able to adapt to fast changes but bacteria with a short generation time can adapt on a shorter timescale allowing the host to cope with fluctuating environment. Gut microbiome plays an important role in an animal’s health and has the potential to improve the management of individuals under human care for conservation purposes.

Generation of self-similar Gaussian time series by means of the DWT and DWPT variance maps

Due to the several kinds of services that use the Internet and data networks infra-structures, the present networks are characterized by the diversity of types of traffic that have statistical properties as complex temporal correlation and non-gaussian distribution. The networks complex temporal correlation may be characterized by the Short Range Dependence (SRD) and the Long Range Dependence - (LRD). Models as the fGN (Fractional Gaussian Noise) may capture the LRD but not the SRD. This work presents two methods for traffic generation that synthesize approximate realizations of the self-similar fGN with SRD random process. The first one employs the IDWT (Inverse Discrete Wavelet Transform) and the second the IDWPT (Inverse Discrete Wavelet Packet Transform). It has been developed the variance map concept that allows to associate the LRD and SRD behaviors directly to the wavelet transform coefficients. The developed methods are extremely flexible and allow the generation of Gaussian time series with complex statistical behaviors.

Time to rehospitalization in patients with schizophrenia discharged on first generation antipsychotics, non-clozapine second generation antipsychotics, or clozapine

Rehospitalization is an important outcome of drug effectiveness in schizophrenia. In this study, the hypothesis that clozapine and some second generation antipsychotics (SGA) were superior to first generation antipsychotics (FGA) in preventing rehospitalization of patients with schizophrenia discharged from a university hospital in Brazil was tested. A retrospective observational study was conducted designed to evaluate time to rehospitalization of patients with schizophrenia discharged on a regimen of oral FGA, depot FGA, risperidone, olanzapine and amisulpride, other SGA, or clozapine, during a three-year follow-up period. Risk factors associated with rehospitalization were examined. Of the 464 patients with schizophrenia discharged from hospital, 242 met criteria for study entry. Higher rehospitalization rates were observed in patients treated with depot FGA (30%), risperidone (30%) and other SGA groups (28.5%), respectively. Clozapine was significantly associated with lower rehospitalization risk compared with risperidone. The risk of rehospitalization in patients on olanzapine and amisulpride, and oral FGA, was similar to that of patients in use of clozapine. These results however, are limited by the heterogeneity of illness severity across the groups. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

A framework for real time MMO game content generation

Com o aumento de plataformas móveis disponíveis no mercado e com o constante incremento na sua capacidade computacional, a possibilidade de executar aplicações e em especial jogos com elevados requisitos de desempenho aumentou consideravelmente. O mercado dos videojogos tem assim um cada vez maior número de potenciais clientes. Em especial, o mercado de jogos massive multiplayer online (MMO) tem-se tornado muito atractivo para as empresas de desenvolvimento de jogos. Estes jogos suportam uma elevada quantidade de jogadores em simultâneo que podem estar a executar o jogo em diferentes plataformas e distribuídos por um "mundo" de jogo extenso. Para incentivar a exploração desse "mundo", distribuem-se de forma inteligente pontos de interesse que podem ser explorados pelo jogador. Esta abordagem leva a um esforço substancial no planeamento e construção desses mundos, gastando tempo e recursos durante a fase de desenvolvimento. Isto representa um problema para as empresas de desenvolvimento de jogos, e em alguns casos, e impraticável suportar tais custos para equipas indie. Nesta tese e apresentada uma abordagem para a criação de mundos para jogos MMO. Estudam-se vários jogos MMO que são casos de sucesso de modo a identificar propriedades comuns nos seus mundos. O objectivo e criar uma framework flexível capaz de gerar mundos com estruturas que respeitam conjuntos de regras definidas por game designers. Para que seja possível usar a abordagem aqui apresentada em v arias aplicações diferentes, foram desenvolvidos dois módulos principais. O primeiro, chamado rule-based-map-generator, contem a lógica e operações necessárias para a criação de mundos. O segundo, chamado blocker, e um wrapper à volta do módulo rule-based-map-generator que gere as comunicações entre servidor e clientes. De uma forma resumida, o objectivo geral e disponibilizar uma framework para facilitar a geração de mundos para jogos MMO, o que normalmente e um processo bastante demorado e aumenta significativamente o custo de produção, através de uma abordagem semi-automática combinando os benefícios de procedural content generation (PCG) com conteúdo gráfico gerado manualmente.

An investigation of the impact of time of generation on carbon savings from PV systems in Great Britain

PV only generates electricity during daylight hours and primarily generates over summer. In the UK, the carbon intensity of grid electricity is higher during the daytime and over winter. This work investigates whether the grid electricity displaced by PV is high or low carbon compared to the annual mean carbon intensity using carbon factors at higher temporal resolutions (half-hourly and daily). UK policy for carbon reporting requires savings to be calculated using the annual mean carbon intensity of grid electricity. This work offers an insight into whether this technique is appropriate. Using half hourly data on the generating plant supplying the grid from November 2008 to May 2010, carbon factors for grid electricity at half-hourly and daily resolution have been derived using technology specific generation emission factors. Applying these factors to generation data from PV systems installed on schools, it is possible to assess the variation in the carbon savings from displacing grid electricity with PV generation using carbon factors with different time resolutions. The data has been analyzed for a period of 363 to 370 days and so cannot account for inter-year variations in the relationship between PV generation and carbon intensity of the electricity grid. This analysis suggests that PV displaces more carbon intensive electricity using half-hourly carbon factors than using daily factors but less compared with annual ones. A similar methodology could provide useful insights on other variable renewable and demand-side technologies and in other countries where PV performance and grid behavior are different.

Labile Plasma Iron Generation After Intravenous Iron is Time-dependent and Transitory in Patients Undergoing Chronic Hemodialysis

Iron supplementation in hemodialysis patients is fundamental to erythropoiesis, but may cause harmful effects. We measured oxidative stress using labile plasma iron (LPI) after parenteral iron replacement in chronic hemodialysis patients. Intravenous iron saccharate (100 mg) was administered in patients undergoing chronic hemodialysis (N = 20). LPI was measured by an oxidant-sensitive fluorescent probe at the beginning of dialysis session (T0), at 10 min (T1), 20 min (T2), and 30 min (T3) after the infusion of iron and at the subsequent session; P < 0.05 was significant. The LPI values were significantly raised according to the time of administration and were transitory: -0.02 +/- 0.20 mu mol/L at the beginning of the first session, 0.01 +/- 0.26 mu mol/L at T0, 0.03 +/- 0.23 mu mol/L at T1, 0.09 +/- 0.28 mmol/L at T2, 0.18 +/- 0.52 mmol/L at T3, and -0.02 +/- 0.16 mmol/L (P = 0.001 to 0.041) at the beginning of the second session. The LPI level in patients without iron supplementation was -0.06 +/- 0.16 mmol/L. Correlations of LPI according to time were T1, T2, and T3 vs. serum iron (P = 0.01, P = 0.007, and P = 0.0025, respectively), and T2 and T3 vs. transferrin saturation (P = 0.001 and P = 0.0003, respectively). LPI generation after intravenous saccharate administration is time-dependent and transitorily detected during hemodialysis. The LPI increment had a positive correlation to iron and transferrin saturation.

Time-series-based maximization of distributed wind power generation integration

Energy policies and technological progress in the development of wind turbines have made wind power the fastest growing renewable power source worldwide. The inherent variability of this resource requires special attention when analyzing the impacts of high penetration on the distribution network. A time-series steady-state analysis is proposed that assesses technical issues such as energy export, losses, and short-circuit levels. A multiobjective programming approach based on the nondominated sorting genetic algorithm (NSGA) is applied in order to find configurations that maximize the integration of distributed wind power generation (DWPG) while satisfying voltage and thermal limits. The approach has been applied to a medium voltage distribution network considering hourly demand and wind profiles for part of the U.K. The Pareto optimal solutions obtained highlight the drawbacks of using a single demand and generation scenario, and indicate the importance of appropriate substation voltage settings for maximizing the connection of MPG.

Evaluating distributed time-varying generation through a multiobjective index

In the last decade, distributed generation, with its various technologies, has increased its presence in the energy mix presenting distribution networks with challenges in terms of evaluating the technical impacts that require a wide range of network operational effects to be qualified and quantified. The inherent time-varying behavior of demand and distributed generation (particularly when renewable sources are used), need to be taken into account since considering critical scenarios of loading and generation may mask the impacts. One means of dealing with such complexity is through the use of indices that indicate the benefit or otherwise of connections at a given location and for a given horizon. This paper presents a multiobjective performance index for distribution networks with time-varying distributed generation which consider a number of technical issues. The approach has been applied to a medium voltage distribution network considering hourly demand and wind speeds. Results show that this proposal has a better response to the natural behavior of loads and generation than solely considering a single operation scenario.