Classification and function prediction of proteins using data compression

Protein has a complicated spatial structure, and has chemical and physical functions which originate from this structure. It is important to predict the structure and function of proteins from a DNA sequence or amino acid sequence from the viewpoint of biology, medical science, protein engineering, etc. However, to data there is no way to predict them accurately from these sequences. Instead, some approaches attempt to estimate the functions based on an approximate similarity in the retrieval of sequences. We propose a new method for the similarity retrieval of an amino acid sequence based on the concept of homology retrieval using data compression. The introduction of compression by a dictionary technique enables us to describe the text data as ann-dimensional vector usingn dictionaries, which is generated by compressingn typical texts, and enables us to classify the proteins based on their similarity. We examined the effectiveness of our proposal using real genome data. This work was presented in part at the Sixth International Symposium on Artificial Life and Robotics, Tokyo, January 15–17, 2001     

A New CMC-AA Resin/Inorganic-gel Super Absorbent Material

A super absorbent material was prepared with the super absorbent resin （ SAR ） and inorganic gel. The SAR of the carboxymethyl cellulose grafting acrylic acid （ CMC-AA ） was copolymer synthesized using the method of inverse-phase suspension polymerization. The influences of the monomer concentration, neutralization degree, the initiator, dispersion agent, cross-linking agent, reaction and drying temperature on the grafting copolymer properties were examined. Meanwhlie, its properties was investigated and the model for absorption mechanism of this absorbent composite was proposed.     

Behavior of Buried Flexible Pipe under High Fills and Design Implications

The existing design guidelines for buried flexible pipes are limited to depth up to 10?m. The increasing use of difficult terrains for infrastructure, landfills, and residential and industrial developments has prompted installation of drainage pipelines under 20–30?m high fills. This paper presents the behavior of an instrumented flexible pipe buried under a 47.1?m deep fill. For filling above 20?m, the measured vertical stress above the pipe exhibited a concave distribution, corresponding to 90 and 110% of the average vertical pressure at the center and edges of the pipe, respectively. The measured results suggest that a triangular lateral pressure distribution can lead to overly conservative and uneconomical results for high fills while Spangler’s analysis is unconservative. Based on the measured results, a revised vertical and lateral earth pressure diagram was proposed for the design of flexible pipe under high fills >20?m. This paper proposes closed-form analyses for estimating the moments and displacements of the pipe subjected to high fill earth pressures. These closed-form solutions agree well with the measured pipe displacements and strains.     

Elution and decomposition of cyanide in soil contaminated with various cyanocompounds

Standard soil samples contaminated with various standard cyanocompounds were prepared. Column elution experiments and analyses were conducted. Compounds with an easy capacity for dissociation to ions, such as KCN and potassium hexacyanoferrate(III), were found to be eluted by forming free cyanide even in fresh water. Hexacyanoferrate(II) salts, such as potassium hexacyanoferrate(II) and iron(III) hexacyanoferrate(II), were found not to be dissociated in water, but were dissociated and diffused under alkaline conditions (pH >13). Hexacyanoferrate(II) ion was found to be more easily dissociated in water with a higher pH.Column tests as above were also conducted for soil samples taken from a former paint ink factory using iron(III) hexacyanoferrate(II), cyanogen chloride, potassium cyanate, copper cyanide, as well as potassium cyanide, as raw materials. It was demonstrate that iron(III) hexacyanoferrate(II) was dissociated and eluted under alkaline conditions. The elution rate was reduced when the contaminated soil was sandwiched with standard soil layers.Further, it was found that the Fe(CN)(6)(4-) ion eluted with NaOH from hexacyanoferrate acid in soil, were easily decomposed into cyanic acid or other byproducts by UV with the addition of ozone and H(2)O(2).     

Fast agglomerative hierarchical clustering algorithm using Locality-Sensitive Hashing

The single linkage method is a fundamental agglomerative hierarchical clustering algorithm. This algorithm regards each point as a single cluster initially. In the agglomeration step, it connects a pair of clusters such that the distance between the nearest members is the shortest. This step is repeated until only one cluster remains. The single linkage method can efficiently detect clusters in arbitrary shapes. However, a drawback of this method is a large time complexity of O(n ²), where n represents the number of data points. This time complexity makes this method infeasible for large data. This paper proposes a fast approximation algorithm for the single linkage method. Our algorithm reduces the time complexity to O(nB) by rapidly finding the near clusters to be connected by Locality-Sensitive Hashing, a fast algorithm for the approximate nearest neighbor search. Here, B represents the maximum number of points going into a single hash entry and it practically diminishes to a small constant as compared to n for sufficiently large hash tables. Experimentally, we show that (1) the proposed algorithm obtains clustering results similar to those obtained by the single linkage method and (2) it runs faster for large data than the single linkage method. Hisashi Koga received the M.S. and Ph.D. degree in information science in 1995 and 2002, respectively, from the University of Tokyo. From 1995 to 2003, he worked as a researcher at Fujitsu Laboratories Ltd. Since 2003, he has been a faculty member at the University of Electro-Communications, Tokyo (Japan). Currently, he is an associate professor at the Graduate School of Information Systems, University of Electro-Communications. His research interest includes various kinds of algorithms such as clustering algorithms, on-line algorithms, and algorithms in network communications. Tetsuo Ishibashi received the M.E. degree in information systems design from the Graduate School of Information Systems at the University of Electro-Communications in 2004. Presently, he is a system engineer at Fujitsu Broad Solution & Consulting Inc. Toshinori Watanabe received the B.E. degree in aeronautical engineering in 1971 and the D.E. degree in 1985, both from the University of Tokyo. In 1971, he worked at Hitachi as a researcher in the field of information systems design. His experience includes demand forecasting, inventory and production management, VLSI design automation, knowledge-based nonlinear optimizer, and a case-based evolutionary learning system nicknamed TAMPOPO. He also engaged in FGCS (Fifth Generation Computer System) project of Japan and developed a new hierarchical message-passing parallel cooperative VLSI layout problem solver that ran on PIM (Parallel Inference Machine) in 1991. Since 1992, he has been a professor at the Graduate School of Information Systems, University of Electro-Communications, Tokyo, Japan. His areas of interest include media analysis, learning intelligence, and the semantics of information systems. He is a member of the IEEE.     

Estimation of forest area near deserts — production of Global Bio-Methanol from solar energy

This paper proposes a new synthesis method for methanol as a future alternative fuel, by the combination of carbon supplied from wood and hydrogen supplied from the electrolysis of water using a solar power generation system in the desert. In the developed countries, more than half of the potential forest area has already been converted into other land uses, while existing forests are well organized and available for wood production. In the developing countries, potential forest sites are expected to be available for wood production, even though they are presently grasslands or secondary forests, while natural tropical forests will not be allowed to be converted into artificial forests. The area available for plantations within 500 km distant from deserts was estimated to be 65 Mha in the world, except for the mountain areas. Biomass production from these sites will be converted annually into 980 Mt methanol with hydrogen from the deserts. This amount is equal to 34% of the world's fuel consumption by vehicles.     

Effect of Support Materials on the Selective Methanation of CO over Ru Catalysts

Selective methanation of CO in the reformate gas (CO/CO₂/H₂/H₂O = 0.175/17.9/70.9/11.1) proceeded over Ru catalysts supported on metal oxides and zeolites. CO was selectively methanated at wide temperature ranges (200–275 °C) over Ru/γ-Al₂O₃, Ru/TiO₂ Ru/H-Y and Ru/H-beta catalysts. Higher Ru contents in Ru/γ-Al₂O₃ improved the selective CO methanation rate.     

Hollow microspheres fabricated from instant adhesive

Non-invasive surgery techniques and drug delivery system with acoustic characteristics of ultrasound contrast agent have been studied intensively in recent years. Many ultrasound contrast agents are commercially available, and they are usually composed of a microbubble coated by a surfactant or lipid bilayer, i.e., a hollow microsphere. We show that the hollow microsphere with polymer shell can be fabricated just blowing vapor of commonly-used instant adhesive into water as microbubbles. The hollow microspheres are composed of cyanoacrylate, a biocompatible material used for adhesion to human tissue such as skin, blood vessels, and organs. Moreover these are less than 10 μm in diameter, which is smaller than a blood capillary (approximately 10 μm). Therefore, with their stable polymer shells, the hollow microspheres are possible ultrasound contrast agents, and are expected to be generated at low cost on the medical frontline, and not in a pharmaceutical factory.     

Development of a Simplified Calculation Tool for Voltage Drop Caused by Transformer Inrush in Distribution System

It is well known that a voltage drop due to inrush current at an energizing transformer may at times interrupt electrical equipment. Generally, the voltage drop is calculated by using a sophisticated tool such as EMTP, so that the transformer saturation phenomenon has been properly represented. However, it is not practical for distribution system engineers to calculate the voltage drop with transformer inrush by using EMTP, because there are many network access requests needing such calculations with many kinds of transformers. Therefore, in this paper, a simplified and easy‐to‐use calculation tool for voltage drops caused by transformer inrush in a distribution system is developed. In order to understand the voltage drop by inrush current during the planning stage, it is formulated by considering the transformer saturation/unsaturation periods in each winding type. The newly developed tool is based on versatile spreadsheet software such as Microsoft Excel ýO.R. It can be used with accuracy similar to that of EMTP. © 2013 Wiley Periodicals, Inc. Electr Eng Jpn, 185(1): 36–47, 2013; Published online in Wiley Online Library ( wileyonlinelibrary.com ). DOI 10.1002/eej.22394