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.     

Optimization of media processing workflows with adaptive operator behaviors

In this paper, we present the ARIA media processing workflow architecture that processes, filters, and fuses sensory inputs and actuates responses in real-time. The components of the architecture are programmable and adaptable; i.e. the delay, size, and quality/precision characteristics of the individual operators can be controlled via a number of parameters. Each data object processed by qStream components is subject to transformations based on the parameter values. For instance, the quality of an output data object and the corresponding processing delay and resource usage depend on the values assigned to parameters of the operators in the object flow path. In Candan, Peng, Ryu, Chatha, Mayer (Efficient stream routing in quality- and resource-adaptive flow architectures. In: Workshop on multimedia information systems, 2004), we introduced a class of flow optimization problems that promote creation and delivery of small delay or small resource-usage objects to the actuators in single-sensor, single-actuator workflows. In this paper, we extend our attention to multi-sensor media processing workflow scenarios. The algorithms we present take into account the implicit dependencies between various system parameters, such as resource consumption and object sizes. We experimentally show the effectiveness and efficiency of the algorithms.

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.     

Parameter-free geometric document layout analysis

Automatic transformation of paper documents into electronic documents requires geometric document layout analysis at the first stage. However, variations in character font sizes, text line spacing, and document layout structures have made it difficult to design a general-purpose document layout analysis algorithm for many years. The use of some parameters has therefore been unavoidable in previous methods. The authors propose a parameter-free method for segmenting the document images into maximal homogeneous regions and identifying them as texts, images, tables, and ruling lines. A pyramidal quadtree structure is constructed for multiscale analysis and a periodicity measure is suggested to find a periodical attribute of text regions for page segmentation. To obtain robust page segmentation results, a confirmation procedure using texture analysis is applied to only ambiguous regions. Based on the proposed periodicity measure, multiscale analysis, and confirmation procedure, we could develop a robust method for geometric document layout analysis independent of character font sizes, text line spacing, and document layout structures. The proposed method was experimented with the document database from the University of Washington and the MediaTeam Document Database. The results of these tests have shown that the proposed method provides more accurate results than previous ones     

Efficient blind dereverberation and echo cancellation based on independent component analysis for actual acoustic signals

This letter presents a new algorithm for blind dereverberation and echo cancellation based on independent component analysis (ICA) for actual acoustic signals. We focus on frequency domain ICA (FD-ICA) because its computational cost and speed of learning convergence are sufficiently reasonable for practical applications such as hands-free speech recognition. In applying conventional FD-ICA as a preprocessing of automatic speech recognition in noisy environments, one of the most critical problems is how to cope with reverberations. To extract a clean signal from the reverberant observation, we model the separation process in the short-time Fourier transform domain and apply the multiple input/output inverse-filtering theorem (MINT) to the FD-ICA separation model. A naive implementation of this method is computationally expensive, because its time complexity is the second order of reverberation time. Therefore, the main issue in dereverberation is to reduce the high computational cost of ICA. In this letter, we reduce the computational complexity to the linear order of the reverberation time by using two techniques: (1) a separation model based on the independence of delayed observed signals with MINT and (2) spatial sphering for preprocessing. Experiments show that the computational cost grows in proportion to the linear order of the reverberation time and that our method improves the word correctness of automatic speech recognition by 10 to 20 points in a RT??= 670 ms reverberant environment.     

An enhanced cross-layer fast handover scheme for mobile IPv6 in the IEEE 802.16e networks

The IEEE 802.16e standard enhances the IEEE 802.16 for the mobility support. Mobile stations can move while receiving services, thus ongoing IP sessions may be maintained during a handover in the IEEE 802.16e. To reduce handover latency, the idea of cross-layer handover which incorporates layer 2 handover with IP layer has been devised. Various cross-layer handover schemes supporting fast handover in the IEEE 802.16e networks have been proposed. However, the problem of the conventional cross-layer fast handover schemes is that they are heavily influenced by the new address confirmation latency which is the most time-consuming procedure. In this paper, we propose an enhanced cross-layer fast handover scheme which is not susceptible to the new address confirmation latency. Detailed performance analysis is performed in terms of the signaling costs and the handover latencies to show the effectiveness of the proposed scheme compared with the conventional ones. The results of the performance evaluation confirm the effectiveness of the proposed scheme.     

A new dimmer for alternating-current directly driven light-emitting-diode lamp

A new dimmer using a mental-oxide-semiconductor field-effect transistor (MOSFET) for alternating-current (AC) directly driven light-emitting-diode (LED) lamp was presented. The control method of proposed dimmer is pulse width control (PWM) method. Compared with the conventional phase-controlled dimmer, the proposed PWM dimmer can produce sine wave and did not cause harmonics problem. Furthermore, the proposed control method did not amplify the light flicker due to the independence of input voltage. Therefore, the PWM dimmer can be used as the dimmer of the AC LED lamp instead of the conventional phase-controlled dimmer. The experimental result shows that the proposed PWM dimmer has good performances.     

Improving Application Launch Performance on Solid State Drives

Application launch performance is of great importance to system platform developers and vendors as it greatly affects the degree of users’ satisfaction.The single most effective way to improve application launch performance is to replace a hard disk drive (HDD) with a solid state drive (SSD),which has recently become affordable and popular.A natural question is then whether or not to replace the traditional HDD-aware application launchers with a new SSD-aware optimizer.We address this question by analyzing the inefficiency of the HDD-aware application launchers on SSDs and then proposing a new SSD-aware application prefetching scheme,called the Fast Application STarter (FAST).The key idea of FAST is to overlap the computation (CPU) time with the SSD access (I/O) time during an application launch.FAST is composed of a set of user-level components and system debugging tools provided by Linux OS (operating system).Hence,FAST can be easily deployed in any recent Linux versions without kernel recompilation.We implement FAST on a desktop PC with an SSD running Linux 2.6.32 OS and evaluate it by launching a set of widely-used applications,demonstrating an average of 28% reduction of application launch time as compared to PC without a prefetcher.     

Loss mechanisms and high power piezoelectrics

Heat generation is one of the significant problems in piezoelectrics for high power density applications. In this paper, we review the loss mechanisms in piezoelectrics first, followed by the heat generation processes for various drive conditions. Heat generation at off-resonance is caused mainly by dielectric loss tan δ′ (i.e., P-E hysteresis loss), not by mechanical loss, while the heat generation at resonance is mainly attributed to mechanical loss tan φ′. Then, practical high power materials developed at Penn State is introduced, which exhibit the vibration velocity more than 1 m/s, leading to the power density capability 10 times of the commercially available “hard” PZTs. We propose a internal bias field model to explain the low loss and high power origin of these materials. Finally, using a low temperature sinterable “hard” PZT, we demonstrated a high power multilayer piezoelectric transformers.     

A new low-cost RF built-in self-test measurement for system-on-chip transceivers

This paper presents a new RF built-in self-test (BIST) measurement and a new automatic-performance-compensation network for a system-on-chip (SoC) transceiver. We built a 5-GHz low noise amplifier (LNA) with an on-chip BIST circuit using 0.18-/spl mu/m SiGe technology. The BIST-measurement circuit contains a test amplifier and RF peak detectors. The complete measurement setup contains an LNA with a BIST circuit, an external RF source, RF relays, 50-/spl Omega/ load impedance, and a dc voltmeter. The proposed BIST circuit measures input impedance, gain, noise figure, input return loss, and output signal-to-noise ratio of the LNA. The test technique utilizes the output dc-voltage measurements, and these measured values are translated to the LNA specifications such as the gain through the developed equations. The performance of the LNA was improved by using the new automatic compensation network (ACN) that adjusts the performance of the LNA with the processor in the SoC transceiver.