BAAQ: an infrastructure for application integration and knowledge discovery in bioinformatics.

The emerging grid computing technologies enable bioinformatics scientists to conduct their researches in a virtual laboratory, in which they share public databases, computational tools as well as their analysis workflows. However, the development of grid applications is still a nightmare for general bioinformatics scientists, due to the lack of grid programming environments, standards and high-level services. Here, we present a system, which we named Bioinformatics: Ask Any Questions (BAAQ), to automate this development procedure as much as possible. BAAQ allows scientists to store and manage remote biological data and programs, to build analysis workflows that integrate these resources seamlessly, and to discover knowledge from available resources. This paper addresses two issues in building grid applications in bioinformatics: how to smoothly compose an analysis workflow using heterogeneous resources and how to efficiently discover and re-use available resources in the grid community. Correspondingly an intelligent grid programming environment and an active solution recommendation service are proposed. Finally, we present a case study applying BAAQ to a bioinformatics problem.     

Land cover in East Asia classified using Terra MODIS and DMSP OLS products

Land cover is classified over East Asia using 250‐m Moderate Resolution Imaging Spectroradiometer (MODIS) land surface reflectance, MODIS snow cover and Operational Linescan System (OLS) human settlement data. The classification method includes a decision tree classification scheme that considers 11 kinds of land surface features derived from the OLS product and the time series of two MODIS products in 2000. The decision tree was defined manually based on the experiment because of insufficient training data, ease of tuning by visual interpretation, and extensibility to further research. The resulting classification is compared to three kinds of reference data, i.e. MODIS land cover product, Chinese digital land cover map, and Chinese census. The land cover classification can be input into a hydrological model applied to the Yellow River in China.     

Development of spectral band cloning techniques for soil nutrients estimation

Satellite‐based monitoring is an indispensable tool to guide soil‐specific crop management. However, it has attained little success in the estimation of soil nutrients due to the limitations incurred from inherent spectral characteristics. In this study, spectral band cloning (SBC) is developed and proposed to augment the soil nutrient predictive capabilities of broadband satellite data. Fine‐spectral channels of spectrometers were synchronized with coarse resolution of IRS satellite data to generate nutrient‐sensitive cloned IRS bands. Soil samples, collected at the time of satellite image acquisition in Lop Buri, Thailand, were analyzed both spectrally and chemically, viz., soil organic matter (OM), phosphorus, potassium and iron. The resulting SBC‐based models showed acceptable correlations, which otherwise were unattainable from raw IRS bands through prevailing models. Accuracy and validation measures showed good agreements between the measured and estimated nutrient surfaces. It is concluded that the SBC is a promising method of quantitative soil nutrient mapping, and could further be used for identification and mapping of other indiscernible biophysical parameters.     

Soil hydraulic parameters estimated from satellite information through data assimilation

Leaf area index (LAI) and actual evapotranspiration (ET_a) from satellite observations were used to estimate simultaneously the soil hydraulic parameters of four soil layers down to 60 cm depth using the combined soil water atmosphere plant and genetic algorithm (SWAP–GA) model. This inverse model assimilates the remotely sensed LAI and/or ET_a by searching for the most appropriate sets of soil hydraulic parameters that could minimize the difference between the observed and simulated LAI (LAI_sim) or simulated ET_a (ET_asim). The simulated soil moisture estimates derived from soil hydraulic parameters were validated using values obtained from soil moisture sensors installed in the field. Results showed that the soil hydraulic parameters derived from LAI alone yielded good estimations of soil moisture at 3 cm depth; LAI and ET_a in combination at 12 cm depth, and ET_a alone at 28 cm depth. There appeared to be no match with measurement at 60 cm depth. Additional information would therefore be needed to better estimate soil hydraulic parameters at greater depths. Despite this inability of satellite data alone to provide reliable estimates of soil moisture at the lowest depth, derivation of soil hydraulic parameters using remote sensing methods remains a promising area for research with significant application potential. This is especially the case in areas of water management for agriculture and in forecasting of floods or drought on the regional scale.     

Updating geomorphic features of watersheds and their boundaries in hazardous areas using satellite synthetic aperture radar

Volcanic disasters can cause severe loss of human life and damage to property. The main damage is caused during an eruption and from subsequent erosion of deposited materials. Heavy rainfall in volcanic areas erodes volcanic deposits, mainly pyroclastic flows and ash fall deposits, which flow as lahar to the foothill of the mountain and cause drastic damage to economically important areas. This post-eruption disaster becomes complex due to the occurrence of stream captures and watershed breakouts that lead to devastating lahars. Continuous monitoring of such geomorphic and hydrologic changes is necessary to cope with changing hazard conditions. Therefore it is important to update the watershed boundaries in order to study current hazard conditions and develop mitigation plans for future disasters. Changes of geomorphic and watershed boundary have occurred in the Mayon Volcano in the Philippines mainly as a result of a major volcanic eruption of 1993, due to which mitigation structures were constructed and modified in the low lying areas. In this study interferometry was used to develop DEM from SAR data to delineate watershed boundaries. New lava flows, pyroclastic flows and lahar deposits in the watersheds were mapped using elevation changes, coherence and intensity derived from the SAR images. Updating geomorphic features of the watersheds and their boundaries using SAR provides a new weather independent alternative technique for monitoring the effect of volcanic activity.     

Esquentian of the mean by three stage procedure

Let X₁, X₂... be i.i.d. observations with mean μ and variance σ², and suppose that given a sample of size n one wishes to estimate μ by X_n, subject to the loss function L_n= A²(X_n-μ)²+n. When σ² is unknown, the optimal sample size n₀ for minimizing the risk R_n = E{L_n} cannotbe found. To resolve this problem, Robbins (1959) proposed a sequential procedure whenX_i is normally distributed, and then the asymptotic properties have been extensively studied. In this paper, we apply Hall's three stage procedure to the problem without specifying the distribution of X_i and derive the second order asymptotic expansions of the expected sample size and the risk.     

sequential estimation of the hgarginal density function for a strongly mixing process

Suppose that {X_n} is a strongly mixing process with unknow marginal density f(x) and that we estimate f(x) by a kernel estimator [fcirc]_n(x|h_n)and want to achive the MISE no larger than some preassigned postive number w. However,the appropriate sample size n^*depends on a functional of the unknow density function. Therefore some sequential procedure is required and we adopt a fully sequential procedure. In this paper we investigate the asymptotic properties of the procedure and show that the producure is asymptotically efficient in a certain sense as w→0. The results are almost the same in the i.i.d. setting. our result extend a class of models to which the methodology can be applied. For example economic variable,experiments on a single subject in which obervation are not indepent, and so on.     

Destruction of volatile organic compounds used in a semiconductorindustry by a capillary tube discharge reactor

Nonthermal plasma technologies offer an innovative approach to the problem of decomposing various volatile organic compounds (VOCs). The authors focused on DC capillary tube discharge plasma reactors to study the decomposition/destruction efficiency for toluene, EGM, trichloroethane and trichloroethylene at 50-2300 ppm levels in dry air. The effects of gas flow rate, VOC concentration and reactor operating conditions on decomposition and analysis of reactant conversion for each VOC were investigated. The results show that VOC destruction efficiency as high as 90% can be achieved, even under a short residence time (3.8 ms) with a destruction energy efficiency of up to 95 g (VOC)/kWh. Laboratory-scale plasma technology was successfully demonstrated for its potential application for VOC control in the semiconductor clean-room environment     

Nanoindentation as a strength probe—a study on the hardness dependence of indent size for fine-grained and coarse-grained ferritic steel

A nanoindentation hardness testing system, including an atomic-force microscope (AFM)-based nanoindentation tester and a calibration method using electrolytically polished single-crystal metals as references, was proposed. This was applied to a study of the mechanical properties of fine-grained ferritic steel (grain size of 1.2 μm) and coarse-grained ferritic steel (30 μm). An empirical function giving the macroscopic hardness for all four reference metals from the nanoindentation force curves was established. The converted Vickers hardness (HV*) of the coarse-grained steel is almost independent of the indent size. The fine-grained steel shows only HV* 130 with an indent of only 100 nm, compared with a macroscopic hardness of HV 210. The difference, HV 80, is considered to reflect the amount of grain-boundary strengthening. The critical indent size for the hardness transition seems to be around 1 μm, comparable to the grain size of the specimen. This result supports the explanation of grainboundary strengthening. It is also consistent with Pickering’s work on low-carbon steel, as the estimated locking parameter (k of 2.6×10⁵ N/m^3/2) in the Hall-Petch relationship is in good agreement with his value of 2.4×10⁵ N/m^3/2.     

Pyrrolizidine Alkaloids Mediate Host-Plant Recognition by Ovipositing Females of an Old World Danaid Butterfly, Idea leuconoe

A giant danaid butterfly, Idea leuconoe, specializes on apocynaceous plants such as Parsonsia laevigata, which has been reported to contain pyrrolizidine alkaloids. Females of I. leuconoe deposited eggs in response to methanolic extract of P. laevigata, and subsequent bioassay-guided fractionation of the extract revealed that phytochemicals crucial for host recognition by ovipositing females are Parsonsia-specific macrocyclic pyrrolizidine alkaloids including parsonsianine, parsonsianidine, and 17-methylparsonsianidine. Parsonine, another P. laevigata pyrrolizidine component with a keto-dihydropyrrolizine moiety that is closely related in structure to male pheromones of the butterfly, and several nonhost pyrrolizidine alkaloids were entirely inactive. We interpret these data as strong evidence for an ancestral association through herbivory between danaid butterflies and pyrrolizidine alkaloids.