Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.

Responses of summertime extreme wave heights to local climate variations in the East China Sea

We detected the responses of summertime extreme wave heights (H-top10, average of the highest 10% of significant wave heights in June, July and August) to local climate variations in the East China Sea by applying an empirical orthogonal function analysis to Htop10 derived from the WAVEWATCH- III wave model driven by 6 hourly sea surface wind fields from ERA-40 reanalysis over the period 1958-2002. Decreases in H-top10 in the northern East China Sea ( Yellow Sea) correspond to attenuation of the East Asian Summer Monsoon, while increases in the south are primarily due to enhancement of tropical cyclone activities in the western North Pacific.

Statistical distribution of depth-integrated local horizontal momentum for second-order random ocean waves in finite water depth

Based on the second-order random wave solutions of water wave equations in finite water depth, statistical distributions of the depth- integrated local horizontal momentum components are derived by use of the characteristic function expansion method. The parameters involved in the distributions can be all determined by the water depth and the wave-number spectrum of ocean waves. As an illustrative example, a fully developed wind-generated sea is considered and the parameters are calculated for typical wind speeds and water depths by means of the Donelan and Pierson spectrum. The effects of nonlinearity and water depth on the distributions are also investigated.

Local warming about 1.3 degrees C in alpine meadow has no effect on root vole (Microtus oeconomus L.) population during winter

The influence of air and soil warming on root vole (Microtus oeconomus L.) population was studied in winter period in top open chambers (OTC) (0.8-1.8 m(2) warmed by conical fiberglass material and situated in alpine meadow (3250 m) at Qinghai-Tibet Plateau, China. The OTCs were distributed on an area of 30 x 30 m of experimental warming site; another site of the same area was a control one. The root vole population was investigated on two pairs of sites in "low-grazing" and "high-grazing" (by sheep) parts of the meadow; mark-recapture method was used. The winter-season averaged air and soil temperature inside of the chambers were 1.3 degrees C higher than the temperature outside the chambers. The warming in the chambers had no statistically significant effect on root vole numbers, on average body mass of individual, and on average body mass of males and females. In conclusion, as small as 1.3 degrees C warming of soil and air introduced locally and on small (several m(2)) scale, in the alpine meadow habitat in winter period, has possibly no effect on root vole numbers and biomass.

Gestão do Comitê de Publicações Local da Embrapa Hortaliças em 2009.

2009

Movimento vertical do herbicida hexazinone em latossolo vermelho distrófico do córrego Espraiado, Ribeirão Preto, SP, cultivado com cana-de-açúcar - simulações considerando dados local e default.

Este trabalho utilizou técnica de simulação computacional para analisar a movimentação vertical do herbicida hexazinone, considerando dados médios default de literatura e dados calculados para suas meia-vida no solo (t½) e coeficiente de adsorção ao carbono orgânico do solo (Koc) em Latossolo Vermelho Distrófico (LVd) do Córrego do Espraiado, Ribeirão Preto-SP. Informações sobre o solo avaliado, climáticas e os dados da cultura de cana-deaçúcar foram utilizadas no simulador CMLS-94. O cenário base de simulação considerou um período de um ano e quatro meses, apresentando data de corte da cultura no mês de agosto e a aplicação de hexazinone, um mês após o corte, na dose de 0,40 kg ha-1, a qual é encontrada em produto comercial utilizado no local. As seguintes profundidades e quantidades finais foram obtidas ao final do período simulado: a) cenário com dado ?default?: 1,89 m e 0,12 kg ha-1; b) cenário com dado local calculado: 2,78 m e 0,18 kg ha-1. Observou-se uma maior movimentação do produto para o cenário simulado com dados locais, principalmente a partir do 63o dia após a aplicação do produto, embora as concentrações tenham se mantido próximas, em ambos cenários. As profundidades alcançadas não comprometem o lençol em sua zona saturada (40m).

Persistent Nodes for Reliable Memory in Geographically Local Networks

A Persistent Node is a redundant distributed mechanism for storing a key/value pair reliably in a geographically local network. In this paper, I develop a method of establishing Persistent Nodes in an amorphous matrix. I address issues of construction, usage, atomicity guarantees and reliability in the face of stopping failures. Applications include routing, congestion control, and data storage in gigascale networks.

Surface Perception from Local Analysis of Texture and Contour

The visual analysis of surface shape from texture and surface contour is treated within a computational framework. The aim of this study is to determine valid constraints that are sufficient to allow surface orientation and distance (up to a multiplicative constant) to be computed from the image of surface texture and of surface contours.

Local Rotational Symmetries

This thesis describes a new representation for two-dimensional round regions called Local Rotational Symmetries. Local Rotational Symmetries are intended as a companion to Brady's Smoothed Local Symmetry Representation for elongated shapes. An algorithm for computing Local Rotational Symmetry representations at multiple scales of resolution has been implemented and results of this implementation are presented. These results suggest that Local Rotational Symmetries provide a more robustly computable and perceptually accurate description of round regions than previous proposed representations. In the course of developing this representation, it has been necessary to modify the way both Smoothed Local Symmetries and Local Rotational Symmetries are computed. First, grey-scale image smoothing proves to be better than boundary smoothing for creating representations at multiple scales of resolution, because it is more robust and it allows qualitative changes in representations between scales. Secondly, it is proposed that shape representations at different scales of resolution be explicitly related, so that information can be passed between scales and computation at each scale can be kept local. Such a model for multi-scale computation is desirable both to allow efficient computation and to accurately model human perceptions.

Apresentação gráfica de parâmetros protéicos utilizando o Java Protein Dossier.

Parâmetros apresentados pelo JPD. Sequência de resíduos. Contatos. Contatos internos. Contatos na interface. Estrutura secundária. Dupla ocupância. Fator de temperatura. Entropia relativa. Confiabilidade. Acessibilidade de resíduos. Ângulos de torsão. Potencial eletrostático. Curvatura na superfície. Hidrofobicidade. Analisando com maior detalhes os parâmetros apresentados.

Crescimento retardado de seringueira plantada como toco alto em faixas abertas em capoeira alta, com enxertia de copa no local de plantio.

Por ser especie heliofila, a seringueira e' plantada em pleno sol. Por esse motivo, foi testado o comportamento de plantio, em trilhas abertas na capoeira, de toco alto que, por medir de 2,10m a 2,40m de altura e possuir maior quantidade de reservas do que as mudas tradicionais, traria as vantagens de reducao do custo de preparo da area, evitando a derruba e queima, com preservacao da materia organica do solo, alem da incorporacao gradual da biomassa da capoeira. As copas de Hevea pauciflora apresentam derrama natural tardia, sugerindo que seu ponto de compensacao luminosa e' mais baixo do que o de H. brasiliensis. Desse modo, copas enxertadas com H. pauciflora poderiam tolerar melhor a fase de crescimento a sombra parcial da capoeira. O tratamento com copa propria apresentou o menor perimetro de caule, com valores tambem baixos nos blocos em pleno sol. Os incrementos anuais em perimetro de caule, apos a decapitacao dos enxerto de copa, permaneceram muito baixos na capoeira, nos tres anos consecutivos, e atingiram valores sucessivamente mais altos em pleno sol, exceto com a copa propria. Os resultados com as copas enxertadas de H. pauciflora demostram, portanto, ser inviavel o plantio em capoeira, nas condicoes descritas neste trabalho.