An energy budget agent-based model of earthworm populations and its application to study the effects of pesticides

Earthworms are important organisms in soil communities and so are used as model organisms in environmental risk assessments of chemicals. However current risk assessments of soil invertebrates are based on short-term laboratory studies, of limited ecological relevance, supplemented if necessary by site-specific field trials, which sometimes are challenging to apply across the whole agricultural landscape. Here, we investigate whether population responses to environmental stressors and pesticide exposure can be accurately predicted by combining energy budget and agent-based models (ABMs), based on knowledge of how individuals respond to their local circumstances. A simple energy budget model was implemented within each earthworm Eisenia fetida in the ABM, based on a priori parameter estimates. From broadly accepted physiological principles, simple algorithms specify how energy acquisition and expenditure drive life cycle processes. Each individual allocates energy between maintenance, growth and/or reproduction under varying conditions of food density, soil temperature and soil moisture. When simulating published experiments, good model fits were obtained to experimental data on individual growth, reproduction and starvation. Using the energy budget model as a platform we developed methods to identify which of the physiological parameters in the energy budget model (rates of ingestion, maintenance, growth or reproduction) are primarily affected by pesticide applications, producing four hypotheses about how toxicity acts. We tested these hypotheses by comparing model outputs with published toxicity data on the effects of copper oxychloride and chlorpyrifos on E. fetida. Both growth and reproduction were directly affected in experiments in which sufficient food was provided, whilst maintenance was targeted under food limitation. Although we only incorporate toxic effects at the individual level we show how ABMs can readily extrapolate to larger scales by providing good model fits to field population data. The ability of the presented model to fit the available field and laboratory data for E. fetida demonstrates the promise of the agent-based approach in ecology, by showing how biological knowledge can be used to make ecological inferences. Further work is required to extend the approach to populations of more ecologically relevant species studied at the field scale. Such a model could help extrapolate from laboratory to field conditions and from one set of field conditions to another or from species to species.

Earthworm distribution and abundance predicted by a process-based model

Earthworms are significant ecosystem engineers and are an important component of the diet of many vertebrates and invertebrates, so the ability to predict their distribution and abundance would have wide application in ecology, conservation and land management. Earthworm viability is known to be affected by the availability and quality of food resources, soil water conditions and temperature, but has not yet been modelled mechanistically to link effects on individuals to field population responses. Here we present a novel model capable of predicting the effects of land management and environmental conditions on the distribution and abundance of Aporrectodea caliginosa, the dominant earthworm species in agroecosystems. Our process-based approach uses individual based modelling (IBM), in which each individual has its own energy budget. Individual earthworm energy budgets follow established principles of physiological ecology and are parameterised for A. caliginosa from experimental measurements under optimal conditions. Under suboptimal conditions (e.g. food limitation, low soil temperatures and water contents) reproduction is prioritised over growth. Good model agreement to independent laboratory data on individual cocoon production and growth of body mass, under variable feeding and temperature conditions support our representation of A. caliginosa physiology through energy budgets. Our mechanistic model is able to accurately predict A. caliginosa distribution and abundance in spatially heterogeneous soil profiles representative of field study conditions. Essential here is the explicit modelling of earthworm behaviour in the soil profile. Local earthworm movement responds to a trade-off between food availability and soil water conditions, and this determines the spatiotemporal distribution of the population in the soil profile. Importantly, multiple environmental variables can be manipulated simultaneously in the model to explore earthworm population exposure and effects to combinations of stressors. Potential applications include prediction of the population-level effects of pesticides and changes in soil management e.g. conservation tillage and climate change.

Functional identity and diversity of animals predict ecosystem functioning better than species-based indices

Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se.

Template-based quadrilateral meshing

Generating quadrilateral meshes is a highly non-trivial task, as design decisions are frequently driven by specific application demands. Automatic techniques can optimize objective quality metrics, such as mesh regularity, orthogonality, alignment and adaptivity; however, they cannot make subjective design decisions. There are a few quad meshing approaches that offer some mechanisms to include the user in the mesh generation process; however, these techniques either require a large amount of user interaction or do not provide necessary or easy to use inputs. Here, we propose a template-based approach for generating quad-only meshes from triangle surfaces. Our approach offers a flexible mechanism to allow external input, through the definition of alignment features that are respected during the mesh generation process. While allowing user inputs to support subjective design decisions, our approach also takes into account objective quality metrics to produce semi-regular, quad-only meshes that align well to desired surface features. Published by Elsevier Ltd.

Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies

Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TR alpha and TR beta. Several pharmacological effects mediated by TR beta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TR beta activation may elicit these effects while maintaining an acceptable safety profile, To understand the molecular determinants of affinity and subtype selectivity of TR ligands, we have successfully employed a ligand- and structure-guided pharmacophore-based approach to obtain the molecular alignment of a large series of thyromimetics. Statistically reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models were obtained using the comparative molecular field analysis (CoMFA) method, and the visual analyses of the contour maps drew attention to a number of possible opportunities for the development of analogs with improved affinity and selectivity. Furthermore, the 3D-QSSR analysis allowed the identification of a novel and previously unmentioned halogen bond, bringing new insights to the mechanism of activity and selectivity of thyromimetics.

Estratégia de operações de redes: uma proposta de abordagem metodológica de investigação para o estudo da relação entre o projeto de rede de negócios, as prioridades competitivas e o valor para o cliente

Nos últimos anos a competição mundial aumentou significativamente o que tem levado a uma maior pressão por flexibilidade nas operações das empresas. Isso causou a mudança das estruturas burocráticas verticais para a organização horizontal, modificando o paradigma prévio, de que a competição se dava entre unidades de negócios. O modelo burocrático tradicional de organização tem se mostrado esgotado, assim a formação de redes de empresas tem possibilitado a emergência de novos modelos organizacionais mais flexíveis. A estratégia de operações, historicamente focada em unidades de negócios, se tornou um campo profícuo para uma nova análise das práticas e modelos existentes. Como a criação e entrega de valor são imprescindíveis para a sobrevivência das redes interfirmas, supõe-se que o valor percebido pelo cliente está conectado com o projeto das organizações em rede. Essa tese propõe, portanto, categorizar as redes simultâneas nas quais as firmas estão inseridas e apresentar uma abordagem metodológica para a investigação da relação entre o valor percebido pelo cliente e o projeto da rede de negócios. Com esse objetivo é conduzido um estudo qualitativo e explanatório das redes simultâneas dentro do campo da estratégia de operações. As conclusões sugerem que o projeto da rede de negócios pesquisada reflete a percepção de valor pelo cliente

Creating buyer-supplier commitment in food supply chains at the base of the pyramid

Esta pesquisa analisa o papel dos aspectos relacionais tais como confiança, comprometimento, interdependência e uso de poder âmbito das estratégias de negócios inclusivos que envolvem pequenos agricultores nas cadeias de valor de multinacionais dos agronegócios no Brasil. Os negócios inclusivos de abastecimento direto por empresas com pequenos agricultores em países em desenvolvimento têm sido reconhecidos como uma abordagem economicamente viavél e promissora para criar impacto social e melhorar as condições de vida de produtores rurais da "base da pirâmide", ao mesmo tempo permitindo que as empresas reforçar as suas posições nos mercados locais e adquirir matérias primas de qualidade a custos mais baixos. Estudos sobre este tema focam amplamente sobre as vantagens comerciais e competitivas que as empresas derivam do abastecimento direito com pequenos fornecedores, apresentando modelos de cadeia de valor customizados e ajustados estratégias globais de negócios, no entanto ainda há pouco conhecimento teoricamente fundamentado sobre os desafios organizacionais e relacionais da relação entre o comprador multinacional e o fornecedor de baixa renda. Além disso, pouco foco tem-se prestado sobre como assimetrias entre multinacionais e produtores de baixa renda, em questão de poder, dependência e de valores pode afetar a evolução dessas relações de negócios. O objetivo do estudo foi descrever os fatores que permitem a esses parceiros assimétricos de construir relacionamentos comerciais de longo prazo e mutuamente benéficos. A metodologia da teoria fundamentada foi usada e foi particularmente adequada para examinar as relações entre comprador e fornecedor e para recolher experiências de campo em três setores principais dominados pela agricultura familiar no Brasil, ou seja laticínios, avi-suinocultura e produção hortícola. Os principais conceitos teóricos da área de Relationship Marketing foram usados para apoiar os resultados da pesquisa de campo. A principal conclusão desta pesquisa é a importância de ir além da construção de confiança na estratégia de gestão do relacionamento entre comprador e fornecedor e de criar parcerias diádicas baseadas na interdependência mútua, a fim de reduzir as assimetrias e melhorar o comprometimento entre a empresa e o pequeno agricultor.

Improved Fault Location on Distribution Feeders Based on Matching During-Fault Voltage Sags

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Molecular models of NS3 protease variants of the Hepatitis C virus

Background: Hepatitis C virus (HCV) currently infects approximately three percent of the world population. In view of the lack of vaccines against HCV, there is an urgent need for an efficient treatment of the disease by an effective antiviral drug. Rational drug design has not been the primary way for discovering major therapeutics. Nevertheless, there are reports of success in the development of inhibitor using a structure-based approach. One of the possible targets for drug development against HCV is the NS3 protease variants. Based on the three-dimensional structure of these variants we expect to identify new NS3 protease inhibitors. In order to speed up the modeling process all NS3 protease variant models were generated in a Beowulf cluster. The potential of the structural bioinformatics for development of new antiviral drugs is discussed.Results: the atomic coordinates of crystallographic structure 1CU1 and 1DY9 were used as starting model for modeling of the NS3 protease variant structures. The NS3 protease variant structures are composed of six subdomains, which occur in sequence along the polypeptide chain. The protease domain exhibits the dual beta-barrel fold that is common among members of the chymotrypsin serine protease family. The helicase domain contains two structurally related beta-alpha-beta subdomains and a third subdomain of seven helices and three short beta strands. The latter domain is usually referred to as the helicase alpha-helical subdomain. The rmsd value of bond lengths and bond angles, the average G-factor and Verify 3D values are presented for NS3 protease variant structures.Conclusions: This project increases the certainty that homology modeling is an useful tool in structural biology and that it can be very valuable in annotating genome sequence information and contributing to structural and functional genomics from virus. The structural models will be used to guide future efforts in the structure-based drug design of a new generation of NS3 protease variants inhibitors. All models in the database are publicly accessible via our interactive website, providing us with large amount of structural models for use in protein-ligand docking analysis.

Measurement of Spin Correlation in t(t)over-bar Production Using a Matrix Element Approach

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Modelling an expert GIS system based on knowledge to evaluate oil spill environmental sensitivity

Oil spills cause great damage to coastal habitats, especially when rapid and suitable response measures are not taken. Establishing high priority areas is fundamental for the operation of response teams. Under this context and considering the need for keeping all geographical information up-to-date for emergencial use, the present study proposes employing a decision tree coupled with a knowledge-based approach using GIS to assign oil sensitivity indices to Brazilian coastal habitats. The modelled system works based on rules set by the official standards of Brazilian Federal Environment Organ. We tested it on one of the littoral regions of Brazil where transportation of petroleum is most intense: the coast of the municipalities of Sao Sebastiao and Caraguatatuba in the northern littoral of São Paulo state, Brazil. The system automatically ranked the littoral sensitivity index of the study area habitats according to geographical conditions during summer and winter; since index ranks of some habitats varied between these seasons because of sediment alterations. The obtained results illustrate the great potential of the proposed system in generating ESI maps and in aiding response teams during emergency operations. (C) 2009 Elsevier Ltd. All rights reserved.

Elastic scattering and the proton form factor

We use the QCD pomeron model proposed by Landshoff and Nachtmann to compute the differential and the total cross-sections for pp scattering in order to discuss a QCD-based approach to the proton form factor. This model is quite dependent on the experimental electromagnetic form factor, and it is not totally clear why this form factor gives good results even at moderate transferred momentum. We exchange the electromagnetic form factor by the asymptotic QCD proton form factor determined by Brodsky and Lepage (BL) plus a prescription for its low energy behavior dictated by the existence of a dynamically generated gluon mass. We fit the data with this QCD inspired form factor and a value for the dynamical gluon mass consistent with the ones determined in the literature. Our results also provide a determination of the proton wave function at the origin, which appears in the BL form factor.

A Harris-Todaro agent-based model to rural-urban migration

The Harris-Todaro model of the rural-urban migration process is revisited under an agent-based approach. The migration of the workers is interpreted as a process of social learning by imitation, formalized by a computational model. By simulating this model, we observe a transitional dynamics with continuous growth of the urban fraction of overall population toward an equilibrium. Such an equilibrium is characterized by stabilization of rural-urban expected wages differential (generalized Harris-Todaro equilibrium condition), urban concentration and urban unemployment. These classic results obtained originally by Harris and Todaro are emergent properties of our model.

Desenvolvimento de método analítico para estudo metabolômico de cana-de-açucar

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Desenvolvimento de métodos de processamento e inteligência computacional no ECG ambulatorial

A monitorização ambulatorial do eletrocardiograma (ECG) permite seguir as atividades cotidianas do paciente durante períodos de 24 horas (ou ainda maiores) possibilitando o estudo de casos que pudessem ter episódios arrítmicos fatais. Entretanto, o maior desafio tecnológico que este tipo de monitorização enfrenta é a perda de informação pela presença de ruídos e artefatos quando o paciente se move. A análise do intervalo QT de despolarização e repolarização ventricular do eletrocardiograma superficial é uma técnica não invasiva com um grande valor para a diagnose e prognósticos de cardiopatias e neuropatias, assim como para a predição da morte cardíaca súbita. A análise do desvio padrão do intervalo QT proporciona informação sobre a dispersão (temporal ou espacial) da repolarização ventricular, entretanto a influencia do ruído provoca erros na detecção do final da onda T que são apreciáveis devido ao fato dos valores pequenos do desvio padrão do QT tanto para sujeitos patológicos e quanto para os sãos. O objetivo geral desta tese é melhorar os métodos de processamento do sinal de ECG ambulatorial usando inteligência computacional, especificamente os métodos relacionados com a detecção do final da onda T, e os de reconhecimento morfológico de batimentos que invalidam a análise da variabilidade do intervalo QT. É proposto e validado (em termos de exatidão e precisão) um novo método e algoritmo para estimar o final da onda T baseado no calculo de áreas de trapézios, empregando sinais da base de dados QT da Physionet. O desempenho do método proposto foi testado e comparado com um dos métodos mais usados para detectar o final da onda T: o método baseado no limiar na primeira derivada. O método de inteligência computacional sugerido combina a extração de características usando o método de análise de componentes principais não lineares e a rede neural de tipo perceptron multicamada. O método de áreas de trapézios teve um bom desempenho em condições ruidosas e não depende de nenhum limiar empírico, sendo adequado para situações com níveis de elevados de ruído de banda larga. O método de reconhecimento morfológico de batimentos foi avaliado com sinais ambulatoriais com e sem artefatos pertencentes a bases de dados de prestigio internacional, e mostrou um bom desempenho.