Pocket extraction on proteins via the Voronoi diagram of spheres

Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, called pockets, on the surface of proteins is important for protein-ligand docking and facilitates fast development of new drugs. Recently, computational approaches have emerged for recognizing pockets from the geometrical point of view. Presented in this paper is a geometric method for the pocket recognition which is based on the Voronoi diagram for atoms. Given a Voronoi diagram, the proposed algorithm transforms the atomic structure to meshes which contain the information of the proximity among atoms, and then recognizes depressions on the surface of a protein using the meshes.     

An Evolutionary Algorithm Approach to Optimal Ensemble Classifiers for DNA Microarray Data Analysis

In general, the analysis of microarray data requires two steps: feature selection and classification. From a variety of feature selection methods and classifiers, it is difficult to find optimal ensembles composed of any feature-classifier pairs. This paper proposes a novel method based on the evolutionary algorithm (EA) to form sophisticated ensembles of features and classifiers that can be used to obtain high classification performance. In spite of the exponential number of possible ensembles of individual feature-classifier pairs, an EA can produce the best ensemble in a reasonable amount of time. The chromosome is encoded with real values to decide the weight for each feature-classifier pair in an ensemble. Experimental results with two well-known microarray datasets in terms of time and classification rate indicate that the proposed method produces ensembles that are superior to individual classifiers, as well as other ensembles optimized by random and greedy strategies.     

Learning type PID control system using input dependence reinforcement scheme

PID control has widely used in the field of process control and a lot of methods have been used to design PID parameters. When the characteristic values of a controlled object are changed due to a change over the years or disturbance, the skilled operators observe the feature of the controlled responses and adjust the PID parameters using their knowledge and know-how, and a lot of labors are required to do it. In this research, we design a learning type PID control system using the stochastic automaton with learning function, namely learning automaton, which can autonomously adjust the control parameters updating the state transition probability using relative amount of controlled error. We show the effectiveness of the proposed learning type PID control system by simulations. This work was presented in part at the 13th International Symposium on Artificial Life and Robotics, Oita, Japan, January 31–February 2, 2008     

Adaptive robust fuzzy control for path tracking of a wheeled mobile robot

This paper proposes an adaptive robust fuzzy control scheme for path tracking of a wheeled mobile robot with uncertainties. The robot dynamics including the actuator dynamics is considered in this work. The presented controller is composed of a fuzzy basis function network (FBFN) to approximate an unknown nonlinear function of the robot complete dynamics, an adaptive robust input to overcome the uncertainties, and a stabilizing control input. The stability and the convergence of the tracking errors are guaranteed using the Lyapunov stability theory. When the controller is designed, the different parameters for two actuator models in the dynamic equation are taken into account. The proposed control scheme does not require the accurate parameter values for the actuator parameters as well as the robot parameters. The validity and robustness of the proposed control scheme are demonstrated through computer simulations. This work was presented in part at the 13th International Symposium on Artificial Life and Robotics, Oita, Japan, January 31–February 2, 2008     

Interactive classification for pre-integrated volume rendering of high-precision volume data

The pre-integrated volume rendering technique is widely used for creating high quality images. It produces good images even though the transfer function is nonlinear. Because the size of the pre-integration lookup table is proportional to the square of data precision, the required storage and computation load steeply increase for rendering of high-precision volume data. In this paper, we propose a method that approximates the pre-integration function proportional to the data precision. Using the arithmetic mean instead of the geometric mean and storing opacity instead of extinction density, this technique reduces the size and the update time of the pre-integration lookup table so that it classifies high-precision volume data interactively. We demonstrate performance gains for typical renderings of volume datasets.     

Suboptimal filter for continuous‐time linear systems with unknown parameters

The filtering problem for continuous‐time linear systems with unknown parameters is considered. A new suboptimal filter is herein proposed. It is based on the optimal mean‐square linear combination of the local Kalman filters. In contrast to the optimal weights, the suboptimal weights do not depend on current observations; thus, the proposed filter can easily be implemented in real‐time. Examples demonstrate high accuracy and efficiency of the suboptimal filter. Copyright © 2008 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society     

Distribution and determinants of maximal physical work capacity of Korean male metal workers

The distribution of maximal physical work capacity (MPWC) can be used to establish an upper limit for energy expenditure during work (EEwork). If physically demanding work has wearing effects, there will be a negative relationship between MPWC and workload. This study was conducted to investigate the distribution of MPWC among Korean metal workers and to examine the relationship between workload and MPWC. MPWC was estimated with a bicycle ergometer using a submaximal test. Energy expenditure was estimated by measuring heart rates during work. The study subjects were 507 male employees from several metal industries in Korea. They had a lower absolute VO2max than the Caucasian populations described in previous studies. The older workers had a lower physical capacity and a greater overload at work. A negative relationship was found between MPWC and workload across all age groups. Upper limits for EEwork for all age groups and for older age groups are recommended based on the 5th percentile value of MPWC.     

Dynamic planning model for determining cutting parameters using neural networks in feature-based process planning

Although feature-based computer-aided process planning plays a vital role in automating and integrating design and manufacturing for efficient production, its off-line properties prohibit the shop floor controllers from rapidly coping with unexpected production errors. The objective of the paper is to suggest a neural network-based dynamic planning model, by which the shop floor controllers determine cutting parameters in real-time based on shop floor status. At off-line is the dynamic planning model constructed as a neural network form, and then embedded into each removal feature. The dynamic planning model will be executed by the shop floor controllers to determine the cutting parameters. A prototype system is constructed to validate whether the dynamic planning model is capable of determining dynamically and efficiently the cutting parameters for a particular set of shop operating factors. Owing to the dynamic planning model, the shop floor controller will increase flexibility and robustness by rapidly and adaptively determining the cutting parameters in unexpected errors occurring.     

The discovery of biomarkers for type 2 diabetic nephropathy by serum proteome analysis

Diabetic nephropathy (DN) is a serious kidney complication of diabetes, and constitutes the leading cause of end-stage renal disease. The earliest clinical evidence of DN is microalbuminuria, a term which refers to the appearance of small but abnormal amounts of albumin in the urine. However, screening methods for DN, such as biomarker assays, are yet to be developed for type 2 DN. In the present study, in an attempt to identify the biomarkers for initial diagnoses of type 2 DN, the protein profiles of human sera collected from 30 microalbuminuric type 2 diabetic patients were compared with those collected from 30 normoalbuminuric type 2 diabetic patients, via 2-DE. As a result, a total of 18 spots were determined to have different protein levels in the microalbuminuric patients. Twelve spots had lower protein levels of approximately 50%, and the other six had higher levels of approximately 100-300% as compared to the spots of normoalbuminuric patients. These spots were identified with ESI-Q-TOF (ESI-quadrupole-TOF) MS. Among the identified proteins, vitamin D-binding protein (DBP) and pigment epithelium-derived factor (PEDF) were verified by Western blotting. The results of this study indicate that the DBP may be employed as diagnostic and monitoring biomarkers of type 2 DN, contingent on further study into the matter.