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.

东海陆架盆地西南部烟囱构造与油气运聚关系研究

In recent years, chimney structure has been proved one of important indicators and a useful guide to major petroleum fields exploration through their exploration history both at home and abroad. Chimney structure, which has been called "gas chimney" or "seismic chimney", is the special fluid-filled fracture swarm, which results from the boiling of active thermal fluid caused by abruptly decreasing of high pressure and high temperature in sedimentary layers of upper lithosphere. Chimney structure is well developed in continental shelf basin of East China Sea, which indicates the great perspectives of petroleum resources there. However, the chimney structure also complicated the petroleum accumulation. So the study of chimney structure on its formation, its effect on occurrence and distribution of petroleum fields is very important not only on theoretical, but also on its applied research. It is for the first time to make a clear definition of chimney structure in this paper, and the existence and practical meaning of chimney structure are illustrated. Firstly, on the viewpoint of exploration, this will amplify exploration area or field, not only in marine, but also on continent. Secondly, this is very important to step-by-step exploration and development of petroleum fields with overpressure. Thirdly, this will provide reference for the study on complex petroleum system with multi-sources, commingled sources and accumulation, multi-stage accumulations, and multi-suits petroleum system in the overlay basin. Fourthly, when the thermal fluid enters the oceanic shallow layer, it can help form gas hydrate under favorable low-temperature and high-pressure conditions. Meanwhile, the thermal fluid with its particular component and thermal content will affect the physical, chemical and ecological environments, which will help solving the problem of global resources and environment. Beginning from the regional tectonic evolution characteristics, this paper discussed the tectonic evolution history of the Taibei depression, then made an dynamical analysis of the tectonic-sedimentary evolution during the Mesozoic and Cenozoic for the East China Sea basin. A numerical model of the tectonic-thermal evolution of the basin via the Basin-Mod technique was carried out and the subsidence-buried history and thermal history of the Taibei depression were inverse calculated: it had undergone a early rapid rift and sag, then three times of uplift and erosion, and finally depressed and been buried. The Taibei depression contains a huge thick clastic sedimentary rock of marine facies, transitional facies and continental facies on the complex basement of ante-Jurassic. It is a part of the back-arc rifting basins occurred during the Mesozoic and Cenozoic. The author analyzed the diagenesis and thermal fluid evolution of this area via the observation of cathodoluminescence, scanning electron microscope and thin section, taking advantage of the evidences of magma activities, paleo-geothermics and structural movement, the author concluded that there were at least three tectonic-thermal events and three epochs of thermal-fluid activities; and the three epochs of thermal-fluid activities were directly relative to the first two tectonic-thermal events and were controlled by the generation and expulsion of hydrocarbon in the source rock simultaneously. Based on these, this paper established the corresponding model between the tectonic-thermal events and the thermal-fluid evolution of the Taibei Depression, which becomes the base for the study on the chimney structures. According to the analyses of the gas-isotope, LAM spectrum component of fluid inclusion, geneses of CO_2 components and geneses of hydrocarbon gases, the author preliminarily verified four sources of the thermal fluid in the Taibei Depression: ① dehydration of mud shale compaction, ② expulsion of hydrocarbon in the source rock; ③ CO_2 gas hydro-thermal decomposition of carbonatite; ④magma-derived thermal fluid including the mantle magma water and volatile components (such as H_2O, CO_2, H_2S, SO_2, N_2 and He etc.). On the basis of the vitrinite reflectance (Ro), homogenization temperature of fluid inclusion, interval transit time of major well-logging, mud density of the wells, measured pressure data and the results of previous studies, this paper analyzed the characteristics of the geothermal fields and geo-pressure fields for the various parts in this area, and discussed the transversal distribution of fluid pressure. The Taibei depression on the whole underwent a temperature-loss process from hot basin to cold basin; and locally high thermal anomalies occurred on the regional background of moderate thermal structure. The seal was primarily formed during the middle and late Paleocene. The overpressured system was formed during the middle and late Eocene. The formation of overpressured system in Lishui Sag underwent such an evolutionary process as "form-weaken-strengthen-weaken". Namely, it was formed during the middle and late Eocene, then was weakened in the Oligocene, even partly broken, then strengthened after the Miocene, and finally weakened. The existence of the thermal fluid rich in volatile gas is a physical foundation for the boiling of the fluid, and sharply pressure depletion was the major cause for the boiling of the fluid, which suggests that there exists the condition for thermal fluid to boil. According to the results of the photoelastic simulation and similarity physical experiments, the geological condition and the formation mechanism of chimnestructures are summarized: well compartment is the prerequisite for chimney formation; the boiling of active thermal fluid is the original physical condition for chimney formation; The local place with low stress by tension fault is easy for chimney formation; The way that thermal fluid migrates is one of the important factors which control the types of chimney structures. Based on where the thermal fluid come from and geometrical characteristics of the chimney structures, this paper classified the genetic types of chimney structures, and concluded that there existed three types and six subtypes chimney structures: organic chimney structures generated by the hydrocarbon-bearing thermal fluid in middle-shallow layers, inorganic and commingling-genetic chimney structures generated by thermal fluid in middle-deep layers. According to the seismic profiles interpretations, well logging response analysis and mineralogical and petrological characteristics in the study area, the author summarized the comprehensive identification marks for chimney structures. Especially the horizon velocity analysis method that is established in this paper and takes advantage of interval velocity anomaly is a semi-quantitative and reliable method of chimney structure s identification. It was pointed out in this paper that the occurrence of the chimney structures in the Taibei depression made the mechanism of accumulation complicated. The author provided proof of episodic accumulation of hydrocarbon in this area: The organic component in the boiling inclusion is the trail of petroleum migration, showing the causality between the boiling of thermal fluid and the chimney structures, meanwhile showing the paroxysmal accumulation is an important petroleum accumulation model. Based on the evolutionary characteristics of various types of chimney structures, this paper discussed their relationships with the migration-accumulation of petroleum respectively. At the same time, the author summarized the accumulating-dynamical models associated with chimney structures. The author analyzed such accumulation mechanisms as the facies state, direction, power of petroleum migration, the conditions of trap, the accumulation, leakage and reservation of petroleum, and the distribution rule of petroleum. The author also provides explanation for such practical problems the existence of a lot of mantle-derived CO_2, and its heterogeneous distribution on plane. By study on and recognition for chimney structure, the existence and distribution of much mantle-derived CO_2 found in this area are explained. Caused by tectonic thermal activities, the deep magma with much CO_2-bearing thermal fluid migrate upward along deep fault and chimney structures, which makes two wells within relatively short distance different gas composition, such as in well LF-1 and well LS36-1-1. Meanwhile, the author predicted the distribution of petroleum accumulation belt in middle-shallow layer for this area, pointed out the three favorable exploration areas in future, and provided the scientific and deciding references for future study on the commingling-genetic accumulation of petroleum in middle-deep layer and the new energy-gas hydrate.

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.

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.