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How is the biological information arranged in genome?

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American Journal of Molecular Biology 2012年第3期2卷 171-186页

作者： masaharu takeda Department of Materials and Biological Engineering Tsuruoka National College of Technology Tsuruoka Yamagata 997-8511 Japan

The four nucleotides (bases), A. T. G and C were sophisticatedly arranged in the structural features in a single-strand of genomic DNA, 1) reverse-complement symmetry of base or base sequences, 2) bias of four bases, 3) multiple fractality of the distribution of each four bases depending on the distance in double logarithmic plot (power spectrum) of L (the distance of a base to the next base) vs. P(L) (the probability of the base-distribution at L), regardless species, forms, genome-sizes and GC-contents. In small genomes such as viruses and plasmids, the multiple fractality might be occasionally hard to distinguish clearly with the power-low-tail region (multi-fractal dimension) because of the low base numbers. In this review article, the author showed that 1) the structural features for the biologically active genomic DNA were observed all living cells including the organelle- and the viralgenome, 2) the potentiality of a new analytical method of the genome structure based on the appearance frequency, Sequence Spectrum Method (SSM) could be analyzed DNA, RNA and protein on genome, 3) the structural features of genome might be related the biological complexity. These findings might be useful extremely to understand the living cells, and the entire genome as a “field” of biological information should need to analyze.

关键词： Entire Genome Biological Information Field Living Cells

Identification of the interactive region by the homology of the sequence spectrum

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Journal of Biomedical Science and Engineering 2010年第9期3卷 868-883页

作者： Masatoshi Nakahara masaharu takeda 不详

The base sequence in genome was governed by some fundamental principles such as reverse-complement symmetry, multiple fractality and so on, and the analytical method of the genome structure, the “Sequence Spectrum Method (SSM)”, based on the structural features of genomic DNA faithfully visualized these principles. This paper reported that the sequence spectrum in SSM closely reflected the biological phenomena of protein and DNA, and SSM could identify the interactive region of protein-protein and DNA-protein uniformly. In order to investigate the effectiveness of SSM we analyzed the several protein-protein and DNA-protein interaction published primarily in the genome of Saccharomyces cerevisiae. The method proposed here was based on the homology of sequence spectrum, and it advantageously and surprisingly used only base sequence of genome and did not require any other information, even information about the amino-acid sequence of protein. Eventually it was concluded that the fundamental principles in genome governed not only the static base sequence but also the dynamic function of protein and DNA.

关键词： Spectrum of Genome Base Sequence Homology of Sequence Spectrum Interactive Region Reverse-Complement Symmetry Multiple Fractality Analytical Method Of Genome

Characterization of the sequence spectrum of DNA based on the appearance frequency of the nucleotide sequences of the genome——A new method for analysis of genome structure

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Journal of Biomedical Science and Engineering 2010年第4期3卷 340-350页

作者： Masatoshi Nakahara masaharu takeda 不详

The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes. Based on the appearance frequency of the key sequences of the genome, any DNA sequences on the genome could be expressed as a sequence spectrum with the adjoining base sequences, which could be used to study the corresponding biological phenomena. In this paper, we used 64 successive three- base sequences (triplets) as the key sequences, and determined and compared the spectra of specific genes to the chromosome, or specific genes to tRNA genes in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Escherichia coli. Based on these analyses, a gene and its corresponding position on the chromosome showed highly similar spectra with the same fold enlargement (approximately 400-fold) in the S. cerevisiae, S. pombe and E. coli genomes. In addition, the homologous structure of genes that encode proteins was also observed with appropriate tRNA gene(s) in the genome. This analytical method might faithfully reflect the encoded biological information, that is, the conservation of the base sequences was to make sense the conservation of the translated amino acids sequence in the coding region, and might be universally applicable to other genomes, even those that consisted of multiple chromosomes.

关键词： Appearance Frequency of Triplet in Genome Base Sequence Self-Similarity Analytical Method of Genome Structure

Gene Organization of F1F0-ATPase Complex in Yeast Saccharomyces cerevisiae.

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Gene Organization of F1F0-ATPase Complex in Yeast Saccharomy...

Effects of Anthropogenic CO2 and Thermally-Induced CO2 on Global Warming

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作者： Katsunori Ohnishi Takuya Yamaguchi Satoshi Nakano Masateru Wakamatsu Hideki Satoh masaharu takeda Dept.Applied Microbial Tech. Kumamoto Inst. Tech.IkedaKumamoto 860-0082Japan Dept.Applied Microbial Tech. Kumamoto Inst. Tech.IkedaKumamoto 860-0082Japan Dept.Applied Microbial Tech. Kumamoto Inst. Tech.IkedaKumamoto 860-0082Japan Dept.Applied Microbial Tech. Kumamoto Inst. Tech.IkedaKumamoto 860-0082Japan Dept.Applied Microbial Tech. Kumamoto Inst. Tech.IkedaKumamoto 860-0082Japan Dept.Applied Microbial Tech. Kumamoto Inst. Tech.IkedaKumamoto 860-0082Japan

＜正＞In yeast S. cerevisiae, five different subunit genes of F1 are encoded by nuclear genomes. The subunit stoichiometry of F1 is generally α3β3γ1δ1ε1 in all organisms although the genetic system is different f...

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Atmospheric and Climate Sciences 2024年第3期14卷 317-327页

作者： masaharu Nishioka Retired Chicago IL USA

Changes in CO2 and temperature are correlated, but it is difficult to observe which is the cause and which is the effect. The release of CO2 dissolved in the ocean into the atmosphere depends on the atmospheric temperature. However, examining the relationship between changes in CO2 caused by other phenomena and temperature is difficult. Studies of soil respiration (Rs) since the late 20th century have shown that CO2 emissions from soil respiration (Rs) are overwhelmingly greater than CO2 emissions from fossil fuel combustion. This is also noted in the IPCC carbon budget assessment. In this paper, the dependences of Rs on temperature, time, latitude, precipitation, seasons, etc., were investigated using the latest NASA database. The changes in temperature and Rs correlated well. There is also a good correlation between Rs and CO2 generation. Therefore, an increase in temperature results in an increase in CO2. On the other hand, there is no evidence other than model calculations that an increase in anthropogenic CO2 is mainly linked to a rise in temperature. The idea that global warming is caused by anthropogenic CO2 production is still a hypothesis. For these reasons, the relationship between global warming and anthropogenic CO2 should be reconsidered based on physical evidence without preconceptions. .

关键词： Global Warming Anthropogenic CO2 Thermally-Induced CO2 Soil Respiration Carbon Cycles

Investigation of HO_(2) uptake mechanisms onto multiple-component ambient aerosols collected in summer and winter time in Yokohama,Japan

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Journal of Environmental Sciences 2024年第3期137卷 18-29页

作者： Jun Zhou Yukiko Fukusaki Kentaro Murano Tania Gautam Yu Bai Yoshimi Inomata Hiroaki Komatsu Mayuko takeda Bin Yuan Min Shao Yosuke Sakamoto Yoshizumi Kajii Institute for Environmental and Climate Research Jinan UniversityGuangzhou 511443China Guangdong-Hongkong-Macao Joint Laboratory of Collaborative Innovation forEnvironmental Quality Guangzhou 511443China Graduate School of Global Environmental Studies Kyoto UniversityKyoto606-8501Japan Yokohama Environmental Science Research Institute Yokohama Kanagawa 221–0024Japan Department of Chemistry University of AlbertaAlbertaEdmonton T6G 2G2Canada Graduate School of Human and Environmental Studies Kyoto UniversityKyoto 606-8501Japan Kanagawa Environmental Research Center Kanagawa 254-0014Japan Center for Regional Environmental Research National Institute for Environmental StudiesIbaraki305-8506Japan

The heterogeneous loss of HO_(2)radicals onto ambient aerosols plays an important role in tropospheric ***,sparse investigation of the dominating parameters controlling the HO_(2)uptake coefficients onto ambient aerosols(γHO_(2))has largely hindered the application of the measuredγHO_(2)to the global spatial *** we induced an offine method using LFP-LIF technique to measure the kinetics of HO_(2)uptake onto ambient aerosols collected in summertime and wintertime in Yokohama city,a regional urban site near Tokyo,*** controlling the dominating parameters which infuenceγHO_(2),we were able to investigate the detailed HO_(2)uptake *** characterized the chemical composition of the collected ambient aerosols,including organics,inorganics,transition metals ions,*** modeledγHO_(2)using different *** show thatγHO_(2)increased with the increase in RH,and the aerosol states(“dry”or wet/aqueous)have large effects onγHO_(2).With fixed RH and aerosol chemical composition,γHO_(2)was highly dependent on pH and inversely correlated with[HO_(2)]_*** combing the measuredγHO_(2)values with the modeled ones,we found that both the HO_(2)self-reaction and transition metal-catalyzed reactions should be accounted for to yield a single parameterization to predictγHO_(2),and different chemical compositions may have collective effects onγHO_(2).Results may serve for extending theγHO_(2)values measured at one observation site to different environmental conditions,which will help us to achieve more accurate modeling results concerning secondary pollutant formation(i.e.,ozone).

关键词： HO_(2)uptake kinetics Offine method Impacting factors Mechanism

Optimized operation scheme of flash-memory-based neural network online training with ultra-high endurance

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Journal of Semiconductors 2024年第1期45卷 33-37页

作者： Yang Feng Zhaohui Sun Yueran Qi Xuepeng Zhan Junyu Zhang Jing Liu masaharu Kobayashi Jixuan Wu Jiezhi Chen School of Information Science and Engineering(ISE) Shandong UniversityQingdao 266200China Neumem Co. LtdHefei 230093China Key Laboratory of Microelectronic Devices and Integrated Technology Institute of Microelectronics of Chinese Academy of SciencesBeijing 100084China Institute of Industrial Science The University of TokyoTokyoJapan

With the rapid development of machine learning,the demand for high-efficient computing becomes more and more *** break the bottleneck of the traditional Von Neumann architecture,computing-in-memory(CIM)has attracted increasing attention in recent *** this work,to provide a feasible CIM solution for the large-scale neural networks(NN)requiring continuous weight updating in online training,a flash-based computing-in-memory with high endurance(10^(9) cycles)and ultrafast programming speed is *** the one hand,the proposed programming scheme of channel hot electron injection(CHEI)and hot hole injection(HHI)demonstrate high linearity,symmetric potentiation,and a depression process,which help to improve the training speed and *** the other hand,the low-damage programming scheme and memory window(MW)optimizations can suppress cell degradation effectively with improved computing *** after 109 cycles,the leakage current(I_(off))of cells remains sub-10pA,ensuring the large-scale computing ability of *** characterizations are done on read disturb to demonstrate its robust *** processing CIFAR-10 tasks,it is evident that~90%accuracy can be achieved after 109 cycles in both ResNet50 and VGG16 *** results suggest that flash-based CIM has great potential to overcome the limitations of traditional Von Neumann architectures and enable high-performance NN online training,which pave the way for further development of artificial intelligence(AI)accelerators.

关键词： NOR flash memory computing-in-memory endurance neural network online training

Prediction of Aerodynamic Noise in a Ring Fan Based on Wake Characteristics

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Journal of Thermal Science 2011年第2期20卷 144-149页

作者： Soichi Sasaki masaharu Fukuda Masao Tsujino Haruhiro Tsubota Faculty of Engineering Nagasaki University 1-14 Bunkyo-machi Nagasaki 852-8521 Japan Graduate School of Science and Technology Nagasaki University 1-14 Bunkyo-machi Nagasaki 852-8521 Japan Research Division Komatsu Ltd.1200 Manda Hiratsuka-shi Kanagawa 254-8567 Japan

A ring fan is a propeller fan that applies an axial-flow impeller with a ring-shaped shroud on the blade tip side. In this study, the entire flow field of the ring fan is simulated using computational fluid dynamics (CFD); the accuracy of the CFD is verified through a comparison with the aerodynamic characteristics of a propeller fan of current model. Moreover, the aerodynamic noise generated by the fan is predicted on the basis of the wake characteristics. The aerodynamic characteristic of the ring fan based on CFD can represent qualitatively the variation in the measured value. The main flow domain of the ring fan is formed at the tip side of the blade because blade tip vortex is not formed at that location. Therefore, the relative velocity of the ring fan is increased by the circumferential velocity. The sound pressure levels of the ring fan within the frequency band of less than 200 Hz are larger than that of the propeller fan. In the analysis of the wake characteristics, it revealed that Karman vortex shedding occurred in the main flow domain in the frequency domain lower than 200 Hz ; the aerodynamic noise of the ring fan in the vortex shedding frequency enlarges due to increase in the relative velocity and the velocity fluctuation.

关键词： Fan Vortex Aerodynamic Noise Wake Internal Flow

Current role of ultrasound for the management of hepatocellular carcinoma

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World Journal of Gastroenterology 2008年第11期14卷 1710-1719页

作者： Hitoshi Maruyama masaharu Yoshikawa Osamu Yokosuka Department of Medicine and Clinical Oncology Chiba University Graduate School of Medicine 1-8-1InohanaChuou-kuChiba 260-8670Japan

Hepatocellular carcinoma （HCC） has a decisive influence on the prognosis of cirrhotic patients. Although α-fetoprotein （AFP） is a known and specific tumor maker for HCC, it is not suitable for the screening and surveillance of HCC because of its poor predictive value and low sensitivity. The use of imaging modalities is essential for the screening, diagnosis and treatment of HCC. Ultrasound （US） plays a major role among them, because it provides real-time and non-invasive observation by a simple and easy technique. In addition, US-guided needle puncture methods are frequently required for the diagnosis and/or treatment process of HCC. The development of digital technology has led to the detection of blood flow by color Doppler US, and the sensitivity for detecting tumor vascularity has shown remarkable improvement with the introduction of microbubble contrast agents. Moreover, near realtime 3-dimensional US images are now available. As for the treatment of HCC, high intensity focused ultrasound （HIFU） was developed as a novel technology that provides transcutaneous ablation effect without needle puncture. These advancements in the US field have led to rapid progress in HCC management, and continuing advances are expected. This article reviews the current application of US for HCC in clinical practice.

关键词： Ultrasound Contrast agent Hepatocellular carcinoma Liver Surveillance Treatments