The binding site distance test score: a robust method for the assessment of predicted protein binding sites

We propose a novel method for scoring the accuracy of protein binding site predictions – the Binding-site Distance Test (BDT) score. Recently, the Matthews Correlation Coefficient (MCC) has been used to evaluate binding site predictions, both by developers of new methods and by the assessors for the community wide prediction experiment – CASP8. Whilst being a rigorous scoring method, the MCC does not take into account the actual 3D location of the predicted residues from the observed binding site. Thus, an incorrectly predicted site that is nevertheless close to the observed binding site will obtain an identical score to the same number of nonbinding residues predicted at random. The MCC is somewhat affected by the subjectivity of determining observed binding residues and the ambiguity of choosing distance cutoffs. By contrast the BDT method produces continuous scores ranging between 0 and 1, relating to the distance between the predicted and observed residues. Residues predicted close to the binding site will score higher than those more distant, providing a better reflection of the true accuracy of predictions. The CASP8 function predictions were evaluated using both the MCC and BDT methods and the scores were compared. The BDT was found to strongly correlate with the MCC scores whilst also being less susceptible to the subjectivity of defining binding residues. We therefore suggest that this new simple score is a potentially more robust method for future evaluations of protein-ligand binding site predictions.

Perceptual grouping and distance estimates in typical and atypical development: comparing performance across perception, drawing and construction tasks

Perceptual grouping is a pre-attentive process which serves to group local elements into global wholes, based on shared properties. One effect of perceptual grouping is to distort the ability to estimate the distance between two elements. In this study, biases in distance estimates, caused by four types of perceptual grouping, were measured across three tasks, a perception, a drawing and a construction task in both typical development (TD: Experiment 1) and in individuals with Williams syndrome (WS: Experiment 2). In Experiment 1, perceptual grouping distorted distance estimates across all three tasks. Interestingly, the effect of grouping by luminance was in the opposite direction to the effects of the remaining grouping types. We relate this to differences in the ability to inhibit perceptual grouping effects on distance estimates. Additive distorting influences were also observed in the drawing and the construction task, which are explained in terms of the points of reference employed in each task. Experiment 2 demonstrated that the above distortion effects are also observed in WS. Given the known deficit in the ability to use perceptual grouping in WS, this suggests a dissociation between the pre-attentive influence of and the attentive deployment of perceptual grouping in WS. The typical distortion in relation to drawing and construction points towards the presence of some typical location coding strategies in WS. The performance of the WS group differed from the TD participants on two counts. First, the pattern of overall distance estimates (averaged across interior and exterior distances) across the four perceptual grouping types, differed between groups. Second, the distorting influence of perceptual grouping was strongest for grouping by shape similarity in WS, which contrasts to a strength in grouping by proximity observed in the TD participants. (c) 2008 Elsevier Inc. All rights reserved.

The effects of institutional distance and headquarters’ financial performance on the generation of environmental standards in multinational companies

This article combines institutional and resources’ arguments to show that the institutional distance between the home and the host country, and the headquarters’ financial performance have a relevant impact on the environmental standardization decision in multinational companies. Using a sample of 135 multinational companies in three different industries with headquarters and subsidiaries based in the USA, Canada, Mexico, France, and Spain, we find that a high environmental institutional distance between headquarters’ and subsidiaries’ countries deters the standardization of environmental practices. On the other hand, high-profit headquarters are willing to standardize their environmental practices, rather than taking advantage of countries with lax environmental protection to undertake more pollution-intensive activities. Finally, we show that headquarters’ financial performance also imposes a moderating effect on the relationship between environmental institutional distance between countries and environmental standardization within the multinational company.

Long-distance dispersal and its influence on adaptation to host resistance in a heterogeneous landscape

Small propagules like pollen or fungal spores may be dispersed by the wind over distances of hundreds or thousands of kilometres,even though the median dispersal may be only a few metres. Such long-distance dispersal is a stochastic event which may be exceptionally important in shaping a population. It has been found repeatedly in field studies that subpopulations of wind-dispersed fungal pathogens virulent on cultivars with newly introduced, effective resistance genes are dominated by one or very few genotypes. The role of propagule dispersal distributions with distinct behaviour at long distances in generating this characteristic population structure was studied by computer simulation of dispersal of clonal organisms in a heterogeneous environment with fields of unselective and selective hosts. Power-law distributions generated founder events in which new, virulent genotypes rapidly colonized fields of resistant crop varieties and subsequently dominated the pathogen population on both selective and unselective varieties, in agreement with data on rust and powdery mildew fungi. An exponential dispersal function, with extremely rare dispersal over long distances, resulted in slower colonization of resistant varieties by virulent pathogens or even no colonization if the distance between susceptible source and resistant target fields was sufficiently large. The founder events resulting from long-distance dispersal were highly stochastic and exact quantitative prediction of genotype frequencies will therefore always be difficult.

The processing of number and gender agreement in Spanish: an event related potential investigation of the effects of structural distance

Previous research suggests that the processing of agreement is affected by the distance between the agreeing elements. However, the unique contribution of structural distance (number of intervening syntactic phrases) to the processing of agreement remains an open question, since previous investigations do not tease apart structural and linear distance (number of intervening words). We used event related potentials (ERPs) to examine the extent to which structural distance impacts the processing of Spanish number and gender agreement. Violations were realized both within the phrase and across the phrase. Across both levels of structural distance, linear distance was kept constant, as was the syntactic category of the agreeing elements. Number and gender agreement violations elicited a robust P600 between 400 and 900ms, a component associated with morphosyntactic processing. No amplitude differences were observed between number and gender violations, suggesting that the two features are processed similarly at the brain level. Within-phrase agreement yielded more positive waveforms than across-phrase agreement, both for agreement violations and for grammatical sentences (no agreement by distance interaction). These effects can be interpreted as evidence that structural distance impacts the establishment of agreement overall, consistent with sentence processing models which predict that hierarchical structure impacts the processing of syntactic dependencies. However, due to the lack of an agreement by distance interaction, the possibility cannot be ruled out that these effects are driven by differences in syntactic predictability between the within-phrase and across-phrase configurations, notably the fact that the syntactic category of the critical word was more predictable in the within-phrase conditions.

Distance measure and the p-median problem in rural areas

The p-median model is used to locate P facilities to serve a geographically distributed population. Conventionally, it is assumed that the population patronize the nearest facility and that the distance between the resident and the facility may be measured by the Euclidean distance. Carling, Han, and Håkansson (2012) compared two network distances with the Euclidean in a rural region witha sparse, heterogeneous network and a non-symmetric distribution of thepopulation. For a coarse network and P small, they found, in contrast to the literature, the Euclidean distance to be problematic. In this paper we extend their work by use of a refined network and study systematically the case when P is of varying size (2-100 facilities). We find that the network distance give as gooda solution as the travel-time network. The Euclidean distance gives solutions some 2-7 per cent worse than the network distances, and the solutions deteriorate with increasing P. Our conclusions extend to intra-urban location problems.

The consequences of the culture aspect and the power distance in the execution of global strategies in multinational companies in Brazil

One of the challenges presented by the current conjecture in Global Companies is to recognize and understand that the culture and levels in structure of the Power Distance in Organizations in different countries contribute, significantly, toward the failure or success of their strategies. The alignment between the implementation and execution of new strategies for projects intended for the success of the Organization as a whole, rather than as an individual part thereof, is an important step towards reducing the impacts of Power Distance (PDI) on the success of business strategies. A position at odds with this understanding by Companies creates boundaries that increase organizational chasms, also taking into consideration relevant aspects such as, FSAs (Firm-Specific Advantages) and CSAs (Country-Specific Advantages). It is also important that the Organizations based in countries or regions of low Power Distance (PDI) between its individuals be more flexible and prepared to ask and to hear the suggestions from Regional and Local Offices. Thus, the purpose of this study is to highlight the elements of effective strategy implementation considering the relevant aspects at all levels of global corporate culture that justify the influences of power distance when implementing new strategies and also to minimize the impacts of this internal business relationship. This study also recognizes that other corporate and cultural aspects are relevant for the success of business strategies so consider, for instance, the lack of alignment between global and regional/local organizations, the need for competent leadership resources, as well as the challenges that indicate the distance between the hierarchical levels ─ Headquarters and Regional Office ─ as some of the various causes that prevent the successful execution of global strategies. Finally, we show that the execution of the strategy cannot be treated as a construction solely created by the Headquarters or by only one Board and that it needs to be understood as a system aimed at interacting with the surroundings.

Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Crossover between the extended and localized regimes in stochastic partially self-avoiding walks in one-dimensional disordered systems

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Electron transfer between adjacent layers in self-assembled films

A simple model of electron transfer is adapted to explain fluorescence quenching in self-assembled films of poly( p-phenylene vinylene) (PPV) alternating with poly(thiophene acetic acid) (PTAA). Quenching is caused by a photo-induced electron transfer between the excited PPV (donor, D) and the PTAA (acceptor, A). The electron-transfer process can be mediated by insertion of electronically inert spacing bilayers between the D and A layers, As the number of bilayers is increased, the fluorescence is gradually recovered which is explained theoretically by assuming that the electron-transfer rate can be described as k = Z exp(- beta r) where r is the distance between D and A. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Effect of denture fabrication and wear on closest speaking space and interocclusal distance during deglutition

Statement of problem. The accuracy of assessing maxillomandibular relationships for trial bases and dentures using phonetic and swallowing methods has not been compared to that observed with definitive prostheses. Thus, there is no evidence to prove whether measurements obtained through such methods remain the same after adaptation to dentures.Purpose. This study investigated changes in the closest speaking space, interocclusal rest space, and interocclusal distance during deglutition in edentulous patients during and after complete denture treatment.Material and methods. Eighteen edentulous subjects participated in this study and measurements were performed after 7 Intervals of time: (1) with occlusion rims and record bases following creation of the maxillomandibular relationship record, (2) with trial dentures, (3) at Insertion of definitive complete dentures, (4) 1 week, (5) 2 weeks, (6) 1 month, and (7) 3 months after insertion. Recordings of interocclusal distances were made with a mandibular kinesiograph. Closest speaking space was measured during the pronunciation of the word 'seis'. The distance between postural rest position and centric occlusion, or interocclusal rest space, was measured using a kinesiograph. Interocclusal distance during deglutition was tested by recording the closest mandibular position recorded during swallowing of 20 mL of water. Data were analyzed using repeated-measure ANOVA, followed by the Student-Newman-Keuls test (alpha=.05).Results. A significant (P <.01)reduction in the mean closest speaking space was found when it was evaluated using occlusion rims and record bases (4.6 mm) compared with other stages (3.0 to 3.4 mm). No significant differences were found in mean interocclusal rest space and interocclusal distance during deglutition among the time periods evaluated.Conclusions. The presence of occlusion rims can influence mandibular position during pronunciation of the /s/ sound. The arrangement of artificial teeth changes the closest speaking space. However, rest position and deglutition were not affected, either during denture fabrication or short-term use.

Charge distribution and calcium affinity of sulfated alpha-L-galactans from ascidians. Comparison between linear and highly branched polymers

Calcium binding and charge distribution on highly branched and linear sulfated L-galactans from ascidians have been studied using a metallochromic indicator and conductimetric titrations. The distance between charged groups of the linear and highly branched galactans does not vary despite their marked differences in sulfate/total sugar molar ratios. These results indicate that the sulfated L-galactose units are concentrated in the central polysaccharide core and not intercalated among non-sulfated units. This inference is consistent with the chemical studies of these galactans. Surprisingly, calcium affinity increases with increasing amounts of non-sulfated sugar branches in the molecule. Thus, calcium binding in these polymers is not a simple function of availability of anion binding sites but a more complex calcium-polysaccharide interaction. (C) 1998 Elsevier B.V. Ltd. All rights reserved.

Effect of thickness of indirect restoration and distance from the light-curing unit tip on the hardness of a dual-cured resin cement

This study evaluated the Knoop hardness and polymerization depth of a dual-cured resin cement, light-activated at different distances through different thicknesses of composite resin. One bovine incisor was embedded in resin and its buccal surface was flattened. Dentin was covered with PVC film where a mold (0.8-mm-thick and 5 mm diameter) was filled with cement and covered with another PVC film. Light curing (40 s) was carried out through resin discs (2, 3, 4 or 5 mm) with a halogen light positioned 0, 1, 2 or 3 mm from the resin surface. After storage, specimens were sectioned for hardness measurements (top, center, and bottom). Data were subjected to split-plot ANOVA and Tukey's test (α=0.05). The increase in resin disc thickness decreased cement hardness. The increase in the distance of the light curing tip decreased hardness at the top region. Specimens showed the lowest hardness values at the bottom, and the highest at the center. Resin cement hardness was influenced by the thickness of the indirect restoration and by the distance between the light-curing unit tip and the resin cement surface.

Põe tapioca, põe farinha d’água?: gastronomia do açaí e identidade socioespacial e cultural na Grande Belém

O presente trabalho teve como objetivo principal analisar as mudanças nas formas de venda e consumo do açaí na Região Metropolitana de Belém (RMB), e sua relação com a identidade de lugar de seus consumidores. O interesse pelo tema teve origem na observação da ocorrência da globalização do açaí, alimento base da dieta das populações amazônicas de origem ribeirinha que hoje é largamente consumido fora da Região Amazônica, em padrões muito diferentes daqueles nela estabelecidos. A escolha da RMB como lócus de pesquisa se justifica pelo fato de que nela se concentra alto consumo de açaí, nos padrões tradicionais e nos modernos, suscitando questionamentos sobre os efeitos dessa convivência na vida cotidiana dos que a habitam. Teoricamente, a pesquisa articula a definição de identidade de lugar de Abe-Lima (2012) com as elaborações de Henri Lefèbvre (1991) sobre a vida cotidiana no mundo moderno e com teoria dos circuitos econômicos de Milton Santos (2008). Metodologicamente, foi adotada uma estratégia multimétodos, envolvendo pesquisa documental, um painel de especialistas com 5 entidades de acompanhamento da produção de açaí, observações pautadas na etnografia urbana em 9 locais de venda e entrevistas semiabertas com 40 consumidores de açaí, maiores de 18 anos e residentes na RMB, recrutados por meio de cadeia tipo bola de neve. Além dos roteiros de entrevistas, foram utilizados como estratégias de coleta de dados diários de campo e fotografias. O conjunto dos dados foi submetido à técnica da análise de conteúdo temática, com eventual apoio do software QDA Miner Lite. Os resultados situaram a globalização do açaí em meados da década de 1990, momento de intensificação dos efeitos da metropolização em Belém, como o aumento populacional, a segregação espacial e a imposição de um ritmo de vida mais acelerado. As análises apontaram que tal processo significou a entrada do açaí no circuito superior da economia, com um processo produtivo mais organizado, utilizando mais tecnologia e envolvendo maiores volumes financeiros, atingindo escala industrial. No entanto, prevalece na RMB o processamento artesanal, em estruturas de pequeno porte, construídas em alvenaria, de organização simples e controle financeiro ausente. O consumo público aumentou, com grande número de locais especializados na oferta de açaí, em caráter de entretenimento, sendo incipiente a adesão a novos acompanhamentos, como granola e aveia. A preferência pelos acompanhamentos tradicionais, como farinha d’água ou de tapioca, açúcar e peixe, permanece, assim como pelo consumo privado, no âmbito da casa, que tem sido favorecido pela disponibilidade do serviço de entrega, recurso recente. A frequência geral de consumo diminuiu, em função do aumento de preço e de mudanças na rotina, como aumento da distância entre local de trabalho e residência. A pesquisa permitiu reafirmar a importância do açaí na vida cotidiana dos belenenses que o consomem, para os quais ele funciona como elemento de distintividade, continuidade, autoestima e autoeficácia, em estreita relação com aspectos próprios da metrópole. Por esse motivo, torna-se preocupante que o acesso a açaí de qualidade, nos padrões desejados pelos indivíduos, esteja tornando-SE privilégio inacessível aos consumidores de menor poder aquisitivo. Assim, espera-se que o conjunto de dados contribua para a compreensão da importância de políticas públicas voltadas ao açaí que considerem melhor as demandas daqueles que o consomem.

Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. (C) 2012 Elsevier Ltd. All rights reserved.