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Searching for protein structure-function relationships using three-dimensional (3D) structural coordinates represents a fundamental approach for determining the function of proteins with unknown functions. Since protein structure databases are rapidly growing in size, the development of a fast search method to find similar protein substructures by comparison of protein 3D structures is essential. In this article, we present a novel protein 3D structure search method to find all substructures with root mean square deviations (RMSDs) to the query structure that are lower than a given threshold value. Our new algorithm runs in O(m + N/m(0.5)) time, after O(N log N) preprocessing, where N is the database size and m is the query length. The new method is 1.8-41.6 times faster than the practically best known O(N) algorithm, according to computational experiments using a huge database (i.e., >20,000,000 C-alpha coordinates). 相似文献
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Tactile displays provoke tactile sensations by artificially stimulating tactile receptors. While many types of tactile displays have been developed, electrotactile displays that exploit electric stimulation can be designed to be thin, light, flexible and thus, wearable. However, the high voltages required to stimulate tactile receptors and limited varieties of possible sensations pose problems. In our previous work, we developed an electrotactile display using a micro-needle electrode array that can drastically reduce the required voltage by penetrating through the high-impedance stratum corneum painlessly, but displaying various tactile sensations was still a challenge. In this work, we demonstrate presentation of tactile sensation of different roughness to the subjects, which is enabled by the arrangement of the electrodes; the needle electrodes are on the fingertip and the ground electrode is on the fingernail. With this arrangement, the display can stimulate the tactile receptors that are located not only in the shallow regions of the finger but also those in the deep regions. It was experimentally revealed that the required voltage was further reduced compared to previous devices and that the roughness presented by the display was controlled by the pulse frequency and the switching time, or the stimulation flow rate. The proposed electrotactile display is readily applicable as a new wearable haptic device for advanced information communication technology. 相似文献
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Mayuko Jomura Yuhei Akashi Hiromu Itoh Risa Yuki Yoshimi Sakai Yutaka Maruyama 《PloS one》2015,10(12)
As a large, long-term pool and source of carbon and nutrients, woody litter is an important component of forest ecosystems. The objective of this study was to estimate the effect of the factors that regulate the rate of decomposition of coarse and fine woody debris (CFWD) of dominant tree species in a cool-temperate forest in Japan. Respiration rates of dead stems, branches, and coarse and fine roots of Fagus crenata and Quercus crispula felled 4 years prior obtained in situ ranged from 20.9 to 500.1 mg CO2 [kg dry wood]–1 h–1 in a one-time measurement in summer. Respiration rate had a significant negative relationship with diameter; in particular, that of a sample of Q. crispula with a diameter of >15 cm and substantial heartwood was low. It also had a significant positive relationship with moisture content. The explanatory variables diameter, [N], wood density, and moisture content were interrelated. The most parsimonious path model showed 14 significant correlations among 8 factors and respiration. Diameter and [C] had large negative direct effects on CFWD respiration rate, and moisture content and species had medium positive direct effects. [N] and temperature did not have direct or indirect effects, and position and wood density had indirect effects. The model revealed some interrelationships between controlling factors. We discussed the influence of the direct effects of explanatory variables and the influence especially of species and position. We speculate that the small R
2 value of the most parsimonious model was probably due to the omission of microbial biomass and activity. These direct and indirect effects and interrelationships between explanatory variables could be used to develop a process-based CFWD decomposition model. 相似文献
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Nakamura Shizuka Fukuma Koichi Wada Kazushige Ueda Mayuko Hayashi Mitsuo 《Sleep and biological rhythms》2018,16(3):351-356
Sleep and Biological Rhythms - The nocturnal sleep of train drivers is apt to be short and their lifestyle become irregular because they drive at midnight and early in the morning. As a result,... 相似文献
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Temporal and spatial changes in gene expression,metabolite accumulation and phytohormone content in rice seedlings grown under drought stress conditions
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Daisuke Todaka Yu Zhao Takuya Yoshida Madoka Kudo Satoshi Kidokoro Junya Mizoi Ken‐Suke Kodaira Yumiko Takebayashi Mikiko Kojima Hitoshi Sakakibara Kiminori Toyooka Mayuko Sato Alisdair R. Fernie Kazuo Shinozaki Kazuko Yamaguchi‐Shinozaki 《The Plant journal : for cell and molecular biology》2017,90(1):61-78
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Hisamitsu Ide Yan Lu Jingsong Yu Takahiro Noguchi Mayuko Kanayama Satoru Muto Raizo Yamaguchi Suguru Kawato Shigeo Horie 《Human cell》2017,30(2):133-139
There is now mounting evidence that the aryl hydrocarbon receptor (AhR) plays an important role in physiologic responses such as development, cell cycle regulation, immune function and also malignant transformation in various tissues. The strong nuclear AhR expression is observed in the invasive phenotype, and an elevated nuclear AhR expression is associated with a poor prognosis of human prostate cancer. On the other hand, there are conflicting results that the AhR deficiency results in increased susceptibility to prostate tumors in mouse model. In the present study, we investigated AhR expression and its role in the growth and invasiveness of human prostate cancer cells. The AhR protein expression was detected in prostate cancer cell lines and human prostate cancer tissues. A small interfering RNA targeting AhR, constitutive active AhR expression vector, and AhR agonist and antagonist were used to moderate its expression and signaling. The induction of AhR signaling attenuated invasiveness of prostate cancer cells without affecting the cellular growth rate. These results suggest that AhR signaling in prostate cancer cells facilitates invasion of these cells, and modulation with this signaling can be a potential therapeutic target of invasive tumors. 相似文献
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Planta - We identified LSG2 as a novel lytic enzyme that accumulates in the parental extracellular matrix and disrupts parental spheroids cooperatively with VheA secreted by juveniles in Volvox.... 相似文献
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Matsunari H Onodera M Tada N Mochizuki H Karasawa S Haruyama E Nakayama N Saito H Ueno S Kurome M Miyawaki A Nagashima H 《Cloning and stem cells》2008,10(3):313-324
Genetically engineered pigs with cell markers such as fluorescent proteins are highly useful in lines of research that include the tracking of transplanted cells or tissues. In this study, we produced transgenic-cloned pigs carrying a gene for the newly developed red fluorescent protein, humanized Kusabira-Orange (huKO), which was cloned from the coral stone Fungia concinna. The nuclear transfer embryos, reconstructed with fetal fibroblast cells that had been transduced with huKO cDNA using retroviral vector DDeltaNsap, developed efficiently in vitro into blastocysts (28.0%, 37/132). Nearly all (94.6%, 35/37) of the cloned blastocysts derived from the transduced cells exhibited clear huKO gene expression. A total of 429 nuclear transfer embryos were transferred to four recipients, all of which became pregnant and gave birth to 18 transgenic-cloned offspring in total. All of the pigs highly expressed huKO fluorescence in all of the 23 organs and tissues analyzed, including the brain, eyes, intestinal and reproductive organs, skeletal muscle, bone, skin, and hoof. Furthermore, such expression was also confirmed by histological analyses of various tissues such as pancreatic islets, renal corpuscles, neuronal and glial cells, the retina, chondrocytes, and hematopoietic cells. These data demonstrate that transgenic-cloned pigs exhibiting systemic red fluorescence expression can be efficiently produced by nuclear transfer of somatic cells retrovirally transduced with huKO gene. 相似文献