Search results for: Daisuke Nakamura

Authors: Daisuke Sagiya, Ren Kamioka

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South Africa has ratified the United Nations Convention on the Rights of Persons with Disabilities (UNCRPD) on 30th November 2007. In line with this, the Department of Social Development (DSD) revised the White Paper on the Rights of Persons with Disabilities (WPRPD), and the Cabinet approved it on 9th December 2015. The South African government is striving towards the elimination of poverty and inequality in line with UNCRPD and WPRPD. However, there are minimal programmes and services that have been provided to persons with disabilities in the rural community. In order to address current discriminative practices, disunity and limited self-representation in rural community, DSD in cooperation with the Japan International Cooperation Agency (JICA) is implementing the 'Project for the Promotion of Empowerment of Persons with Disabilities and Disability Mainstreaming' from May 2016 to May 2020. The project is targeting rural community as the project sites, namely 1) Collins Chabane municipality, Vhembe district, Limpopo and 2) Maluti-a-Phofung municipality, Thabo Mofutsanyana district, Free State. The project aims at developing good practices on Community-Based Inclusive Development (CBID) at the project sites which will be documented as a guideline and applied in other provinces in South Africa and neighbouring countries (Lesotho, Swaziland, Botswana, Namibia, Zimbabwe, and Mozambique). In cooperation with provincial and district DSD and local government, the project is currently implementing various community activities, for example: Establishment of Self-Help Group (SHG) of persons with disabilities and Peer Counselling in the villages, and will conduct Disability Equality Training (DET) and accessibility workshop in order to enhance the CBID in the project sites. In order to universalise good practices on CBID, the authors will explain lessons learned from the project by utilising the theories of disability and development studies and community psychology such as social model of disability, twin-track approach, empowerment theory, sense of community, helper therapy principle, etc. And the authors conclude that in order to realise social participation of persons with disabilities in rural community, CBID is a strong tool and persons with disabilities must play central roles in all spheres of CBID activities.

Keywords: community-based inclusive development, disability mainstreaming, empowerment of persons with disabilities, self-help group

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Authors: Fumiya Sugino, Naohiro Nakamura, Yuji Miyazu

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In earthquake resistant design of buildings, evaluation of vibration characteristics is important. In recent years, due to the increment of super high-rise buildings, the evaluation of response is important for not only the first mode but also higher modes. The knowledge of vibration characteristics in buildings is mostly limited to the first mode and the knowledge of higher modes is still insufficient. In this paper, using earthquake observation records of a SRC building by applying frequency filter to ARX model, characteristics of first and second modes were studied. First, we studied the change of the eigen frequency and the damping ratio during the 3.11 earthquake. The eigen frequency gradually decreases from the time of earthquake occurrence, and it is almost stable after about 150 seconds have passed. At this time, the decreasing rates of the 1st and 2nd eigen frequencies are both about 0.7. Although the damping ratio has more large error than the eigen frequency, both the 1st and 2nd damping ratio are 3 to 5%. Also, there is a strong correlation between the 1st and 2nd eigen frequency, and the regression line is y=3.17x. In the damping ratio, the regression line is y=0.90x. Therefore 1st and 2nd damping ratios are approximately the same degree. Next, we study the eigen frequency and damping ratio from 1998 after 3.11 earthquakes, the final year is 2014. In all the considered earthquakes, they are connected in order of occurrence respectively. The eigen frequency slowly declined from immediately after completion, and tend to stabilize after several years. Although it has declined greatly after the 3.11 earthquake. Both the decresing rate of the 1st and 2nd eigen frequencies until about 7 years later are about 0.8. For the damping ratio, both the 1st and 2nd are about 1 to 6%. After the 3.11 earthquake, the 1st increases by about 1% and the 2nd increases by less than 1%. For the eigen frequency, there is a strong correlation between the 1st and 2nd, and the regression line is y=3.17x. For the damping ratio, the regression line is y=1.01x. Therefore, it can be said that the 1st and 2nd damping ratio is approximately the same degree. Based on the above results, changes in eigen frequency and damping ratio are summarized as follows. In the long-term study of the eigen frequency, both the 1st and 2nd gradually declined from immediately after completion, and tended to stabilize after a few years. Further it declined after the 3.11 earthquake. In addition, there is a strong correlation between the 1st and 2nd, and the declining time and the decreasing rate are the same degree. In the long-term study of the damping ratio, both the 1st and 2nd are about 1 to 6%. After the 3.11 earthquake, the 1st increases by about 1%, the 2nd increases by less than 1%. Also, the 1st and 2nd are approximately the same degree.

Keywords: eigenfrequency, damping ratio, ARX model, earthquake observation records

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Authors: Ami Okabe, Daisuke Gondo, Akira Ogawa, Yasuhisa Hasegawa, Koichi Sato, Sadao Araki, Hideki Yamamoto

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Membrane separation draws attention as the energy-saving technology. Pervaporation (PV) uses hydrophobic ceramic membranes to separate organic compounds from industrial wastewaters. PV makes it possible to separate organic compounds from azeotropic mixtures and from aqueous solutions. For the PV separation of low concentrations of organics from aqueous solutions, hydrophobic ceramic membranes are expected to have high separation performance compared with that of conventional hydrophilic membranes. Membrane separation performance is evaluated based on the pervaporation separation index (PSI), which depends on both the separation factor and the permeate flux. Ingenuity is required to increase the PSI such that the permeate flux increases without reducing the separation factor or to increase the separation factor without reducing the flux. A thin separation layer without defects and pinholes is required. In addition, it is known that the flux can be increased without reducing the separation factor by reducing the diffusion resistance of the membrane support. In a previous study, we prepared hydrophobic silica membranes by a molecular templating sol−gel method using cetyltrimethylammonium bromide (CTAB) to form pores suitable for permitting the passage of organic compounds through the membrane. We separated low-concentration organics from aqueous solutions by PV using these membranes. In the present study, hydrophobic silica membranes were prepared on a porous alumina hollow fiber support that is thinner than the previously used alumina support. Ethyl acetate (EA) is used in large industrial quantities, so it was selected as the organic substance to be separated. Hydrophobic silica membranes were prepared by dip-coating porous alumina supports with a -alumina interlayer into a silica sol containing CTAB and vinyltrimethoxysilane (VTMS) as the silica precursor. Membrane thickness increases with the lifting speed of the sol in the dip-coating process. Different thicknesses of the γ-alumina layer were prepared by dip-coating the support into a boehmite sol at different lifting speeds (0.5, 1, 3, and 5 mm s-1). Silica layers were subsequently formed by dip-coating using an immersion time of 60 s and lifting speed of 1 mm s-1. PV measurements of the EA (5 wt.%)/water system were carried out using VTMS hydrophobic silica membranes prepared on -alumina layers of different thicknesses. Water and EA flux showed substantially constant value despite of the change of the lifting speed to form the γ-alumina interlayer. All prepared hydrophobic silica membranes showed the higher PSI compared with the hydrophobic membranes using the previous alumina support of hollow fiber.

Keywords: membrane separation, pervaporation, hydrophobic, silica

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Authors: Guo Lei, Wang Yue, Nakamura Yoshio, Shi Ji

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Recently, perpendicular exchange bias (PEB) is introduced as an active topic attracting continuous efforts. Since its discovery, extrinsic control of PEB has been proposed, due to its scientific significance in spintronic devices and potential application in high density magnetic random access memory with perpendicular magnetic tunneling junction (p-MTJ). To our knowledge, the researches aiming to controlling PEB so far are focused mainly on enhancing the interfacial exchange coupling by adjusting the FM/AFM interface roughness, or optimizing the crystalline structures of FM or AFM layer by employing different seed layers. In present work, the effects of magnetoelastically induced PMA on PEB have been explored in [CoO5nm/CoPt5nm]5 multilayer films. We find the PMA strength of FM layer also plays an important role on PEB at the FM/AFM interface and it is effective to control PEB of [CoO5nm/CoPt5nm]5 multilayer films by changing the magnetoelastically induced PMA of CoPt layer. [CoO5nm/CoPt5nm]5 multilayer films were deposited by magnetron sputtering on fused quartz substrate at room temperature, then annealed at 100°C, 250°C, 300°C and 375°C for 3h, respectively. XRD results reveal that all the samples are well crystallized with preferred fcc CoPt (111) orientation. The continuous multilayer structure with sharp component transition at the CoO5nm/CoPt5nm interface are identified clearly by transmission electron microscopy (TEM), x-ray reflectivity (XRR) and atomic force microscope (AFM). CoPt layer in-plane tensile stress is calculated by sin2φ method, and we find it increases gradually upon annealing from 0.99 GPa (as-deposited) up to 3.02 GPa (300oC-annealed). As to the magnetic property, significant enhancement of PMA is achieved in [CoO5nm/CoPt5nm]5 multilayer films after annealing due to the increase of CoPt layer in-plane tensile stress. With the enhancement of magnetoelastically induced PMA, great improvement of PEB is also achieved in [CoO5nm/CoPt5nm]5 multilayer films, which increases from 130 Oe (as-deposited) up to 1060 Oe (300oC-annealed), showing the same change tendency as PMA and the strong correlation with CoPt layer in-plane tensile stress. We consider it is the increase of CoPt layer in-plane tensile stress that leads to the enhancement of PMA, and thus the enhancement of magnetoelastically induced PMA results in the improvement of PEB in [CoO5nm/CoPt5nm]5 multilayer films.

Keywords: perpendicular exchange bias, magnetoelastically induced perpendicular magnetic anisotropy, CoO5nm/CoPt5nm]5 multilayer film with in-plane stress, perpendicular magnetic tunneling junction

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Authors: Sadao Araki, Daisuke Gondo, Satoshi Imasaka, Hideki Yamamoto

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The separation of organic compounds from aqueous solutions is a key technology for recycling valuable organic compounds and for the treatment of wastewater. The wastewater from chemical plants often contains organic compounds such as ethyl acetate (EA), methylethyl ketone (MEK) and isopropyl alcohol (IPA). In this study, we prepared hydrophobic silica membranes by a sol-gel method. We used phenyltrimethoxysilane (PhTMS), ethyltrimethoxysilan (ETMS), Propyltrimethoxysilane (PrTMS), N-butyltrimethoxysilane (BTMS), N-Hexyltrimethoxysilane (HTMS) as silica sources to introduce each functional groups on the membrane surface. Cetyltrimethyl ammonium bromide (CTAB) was used as a molecular template to create suitable pore that enable the permeation of organic compounds. These membranes with five different functional groups were characterized by SEM, FT-IR, and permporometry. Thicknesses and pore diameters of silica layer for all membrane were about 1.0 μm and about 1 nm, respectively. In other words, functional groups had an insignificant effect on the membrane thicknesses and the formation of the pore by CTAB. We confirmed the effect of functional groups on the flux and separation factor for ethyl acetate (EA), methyl ethyl ketone, acetone and 1-butanol (1-BtOH) /water mixtures. All membranes showed a high flux for ethyl acetate compared with other compounds. In particular, the hydrophobic silica membrane prepared by using BTMS showed 0.75 kg m-2 h-1 of flux for EA. For all membranes, the fluxes of organic compounds showed the large values in the order corresponding to EA > MEK > acetone > 1-BtOH. On the other hand, carbon chain length of functional groups among ETMS, PrTMS, BTMS, PrTMS and HTMS did not have a major effect on the organic flux. Although we confirmed the relationship between organic fluxes and organic molecular diameters or fugacity of organic compounds, these factors had a low correlation with organic fluxes. It is considered that these factors affect the diffusivity. Generally, permeation through membranes is based on the diffusivity and solubility. Therefore, it is deemed that organic fluxes through these hydrophobic membranes are strongly influenced by solubility. We tried to estimate the organic fluxes by Hansen solubility parameter (HSP). HSP, which is based on the cohesion energy per molar volume and is composed of dispersion forces (δd), intermolecular dipole interactions (δp), and hydrogen-bonding interactions (δh), has recently attracted attention as a means for evaluating the resolution and aggregation behavior. Evaluation of solubility for two substances can be represented by using the Ra [(MPa)1/2] value, meaning the distance of HSPs for both of substances. A smaller Ra value means a higher solubility for each substance. On the other hand, it can be estimated that the substances with large Ra value show low solubility. We established the correlation equation, which was based on Ra, of organic flux at low concentrations of organic compounds and at 295-325 K.

Keywords: hydrophobic, membrane, Hansen solubility parameter, functional group

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Authors: Waheed Ahmad Safi, Shunichi Nakamura

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Concrete filled steel I-girder (CFIG) bridge was proposed and the bending and shear strength was confirmed by experiments. The area surrounded by the upper and lower flanges and the web is filled with concrete in CFIG, which is used to the intermediate support of a continuous girder. Three-dimensional finite element models were established to simulate the bending and shear behaviors of CFIG and to clarify the load transfer mechanism. Steel plates and filled concrete were modeled as a three-dimensional 8-node solid element and steel reinforcement bars as a three-dimensional 2-node truss element. The elements were mostly divided into the 50 x 50 mm mesh size. The non-linear stress-strain relation is assumed for concrete in compression including the softening effect after the peak, and the stress increases linearly for concrete in tension until concrete cracking but then decreases due to tension stiffening effect. The stress-strain relation for steel plates was tri-linear and that for reinforcements was bi-linear. The concrete and the steel plates were rigidly connected. The developed FEM model was applied to simulate and analysis the bending behaviors of the CFIG specimens. The vertical displacements and the strains of steel plates and the filled concrete obtained by FEM agreed very well with the test results until the yield load. The specimens collapsed when the upper flange buckled or the concrete spalled off. These phenomena cannot be properly analyzed by FEM, which produces a small discrepancy at the ultimate states. The FEM model was also applied to simulate and analysis the shear tests of the CFIG specimens. The vertical displacements and strains of steel and concrete calculated by FEM model agreed well with the test results. A truss action was confirmed by the FEM and the experiment, clarifying that shear forces were mainly resisted by the tension strut of the steel plate and the compression strut of the filled concrete acting in the diagonal direction. A trail design with the CFIG was carried out for a four-span continuous highway bridge and the design method was established. Construction cost was estimated about 12% lower than that of a conventional steel I-section girder.

Keywords: concrete filled steel I-girder, bending strength, FEM, limit states design, steel I-girder, shear strength

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Authors: Takeru Furuawa, Kohei Takizawa, Daisuke Kuwahara, Shunjiro Shinohara

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In the field of a space propulsion, an electric propulsion system has been developed because its fuel efficiency is much higher than a conventional chemical one. However, the practical electric propulsion systems, e.g., an ion engine, have a problem of short lifetime due to a damage of generation and acceleration electrodes of the plasma. A helicon plasma thruster is proposed as a long-lifetime electric thruster which has non-direct contact electrodes. In this system, both generation and acceleration methods of a dense plasma are executed by antennas from the outside of a discharge tube. Development of the helicon plasma thruster has been conducting under the Helicon Electrodeless Advanced Thruster (HEAT) project. Our helicon plasma thruster has two important processes. First, we generate a dense source plasma using a helicon wave with an excitation frequency between an ion and an electron cyclotron frequencies, fci and fce, respectively, applied from the outside of a discharge using a radio frequency (RF) antenna. The helicon plasma source can provide a high-density (~1019 m-3), a high-ionization ratio (up to several tens of percent), and a high particle generation efficiency. Second, in order to achieve high thrust and specific impulse, we accelerate the dense plasma by the axial Lorentz force fz using the product of the induced azimuthal current jθ and the static radial magnetic field Br, shown as fz = jθ × Br. The HEAT project has proposed several kinds of electrodeless acceleration schemes, and in our particular case, a Rotating Magnetic Field (RMF) method has been extensively studied. The RMF scheme was originally developed as a concept to maintain the Field Reversed Configuration (FRC) in a magnetically confined fusion research. Here, RMF coils are expected to generate jθ due to a nonlinear effect shown below. First, the rotating magnetic field Bω is generated by two pairs of RMF coils with AC currents, which have a phase difference of 90 degrees between the pairs. Due to the Faraday’s law, an axial electric field is induced. Second, an axial current is generated by the effects of an electron-ion and an electron-neutral collisions through the Ohm’s law. Third, the azimuthal electric field is generated by the nonlinear term, and the retarding torque generated by the collision effects again. Then, azimuthal current jθ is generated as jθ = - nₑ er ∙ 2π fRMF. Finally, the axial Lorentz force fz for plasma acceleration is generated. Here, jθ is proportional to nₑ and frequency of RMF coil current fRMF, when Bω is fully penetrated into the plasma. Our previous study has achieved 19 % increase of ion velocity using the 5 MHz and 50 A of the RMF coil power supply. In this presentation, we will show the improvement of the ion velocity using the lower frequency and higher current supplied by RMF power supply. In conclusion, helicon high-density plasma production and electromagnetic acceleration by the RMF scheme with a concept of electrodeless condition have been successfully executed.

Keywords: electric propulsion, electrodeless thruster, helicon plasma, rotating magnetic field

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Authors: Naohiro Nakamura, Takuya Kinoshita, Hiroshi Fukuyama

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The 2011 off The Pacific Coast of Tohoku Earthquake caused considerable damage to wide areas of eastern Japan. A large number of earthquake observation records were obtained at various places. To design more earthquake-resistant buildings and improve earthquake disaster prevention, it is necessary to utilize these data to analyze and evaluate the behavior of a building during an earthquake. This paper presents an earthquake response simulation analysis (hereafter a seismic response analysis) that was conducted using data recorded during the main earthquake (hereafter the main shock) as well as the earthquakes before and after it. The data were obtained at a high-rise steel-reinforced concrete (SRC) building in the bay area of Tokyo. We first give an overview of the building, along with the characteristics of the earthquake motion and the building during the main shock. The data indicate that there was a change in the natural period before and after the earthquake. Next, we present the results of our seismic response analysis. First, the analysis model and conditions are shown, and then, the analysis result is compared with the observational records. Using the analysis result, we then study the effect of soil-structure interaction on the response of the building. By identifying the characteristics of the building during the earthquake (i.e., the 1st natural period and the 1st damping ratio) by the Auto-Regressive eXogenous (ARX) model, we compare the analysis result with the observational records so as to evaluate the accuracy of the response analysis. In this study, a lumped-mass system SR model was used to conduct a seismic response analysis using observational data as input waves. The main results of this study are as follows: 1) The observational records of the 3/11 main shock put it between a level 1 and level 2 earthquake. The result of the ground response analysis showed that the maximum shear strain in the ground was about 0.1% and that the possibility of liquefaction occurring was low. 2) During the 3/11 main shock, the observed wave showed that the eigenperiod of the building became longer; this behavior could be generally reproduced in the response analysis. This prolonged eigenperiod was due to the nonlinearity of the superstructure, and the effect of the nonlinearity of the ground seems to have been small. 3) As for the 4/11 aftershock, a continuous analysis in which the subject seismic wave was input after the 3/11 main shock was input was conducted. The analyzed values generally corresponded well with the observed values. This means that the effect of the nonlinearity of the main shock was retained by the building. It is important to consider this when conducting the response evaluation. 4) The first period and the damping ratio during a vibration were evaluated by an ARX model. Our results show that the response analysis model in this study is generally good at estimating a change in the response of the building during a vibration.

Keywords: ARX model, response analysis, SRC building, the 2011 off the Pacific Coast of Tohoku Earthquake

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Authors: Kuniko Muramoto, Tadashi Nakamura, Shiro Dan

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On March 11, 2011 the Great East Japan Disaster caused widespread damage. In the aftermath, we searched for ways to provide long-term support and enhanced resilience to affected areas, arriving at the Family Manga Exhibition: an art collection portraying family life. It became a tool for community outreach and intervention, and we implemented support programs by collaborating with local support agencies. This 10-year project has been touring through four prefectures in Tohoku since the disaster struck, bearing witness to the effects of disaster and recovery alike. At this five-year mark, we use a narrative perspective to present our findings and reflect on post-disaster community support. It is important to note that the exhibition’s art does not directly depict the disaster; it portrays stories of anonymous families instead. They stimulate viewers’ memories and remind them of their own family stories. We analyzed viewers' oral and written responses to the exhibition and discovered that family manga as an art form enhances the viewer’s sense of connection to people close to them. We also discovered that the viewers gained more universal perspective on their own situations by viewing the exhibition. Manga, we found, offered a certain safety by enabling the viewers to control how they would interact with the exhibition's content and themes. In addition, the purpose of the project was for us to become witnesses of the disaster and recovery. Supporters of the project became active listeners, functioning as interactive agents who helped forming stories. Voices of the story tellers and the listeners layered upon each other and, as a result, converged into brand new narratives. The essence of traumatic experience is ‘the sense of overwhelming powerlessness and isolation’. When we redefine trauma as ‘broken relationships’, we can say that ‘enhancing relationships’ and ‘weaving relationships’ are what strengthen our resilience. This project used narrative as a modality to fortify the resilience of people involved by enhancing the social capital of bonding, bridging, and linking. The manga exhibition functioned as a tool to achieve this end, suggesting that similar applications are possible. Programs we held in-between manga exhibitions also served to enhance narratives of resiliency in the regions. However, we will save that story for another time. We hope to continue collecting the precious and polyphonic voices of people to present as stories born out of the Great East Japan Disaster. This effort extends beyond the immediately affected area by helping us prepare our resilience for future disasters.

Keywords: community, manga, narrative, resilience

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Authors: Shinji Ukita, Naohiro Nakamura, Yuji Miyazu

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In considering the dynamic characteristics of structure, natural frequency and damping ratio are useful indicator. When performing dynamic design, it's necessary to select an appropriate initial damping model and hysteretic model. In the linear region, the setting of initial damping model influences the response, and in the nonlinear region, the combination of initial damping model and hysteretic model influences the response. However, the dynamic characteristics of structure in the nonlinear region remain unclear. In this paper, we studied the effect of setting of initial damping model and hysteretic model on the dynamic characteristics of structure. On initial damping model setting, Initial stiffness proportional, Tangent stiffness proportional, and Rayleigh-type were used. On hysteretic model setting, TAKEDA model and Normal-trilinear model were used. As a study method, dynamic analysis was performed using a lumped mass model of base-fixed. During analysis, the maximum acceleration of input earthquake motion was gradually increased from 1 to 600 gal. The dynamic characteristics were calculated using the ARX model. Then, the characteristics of 1st and 2nd natural frequency and 1st damping ratio were evaluated. Input earthquake motion was simulated wave that the Building Center of Japan has published. On the building model, an RC building with 30×30m planes on each floor was assumed. The story height was 3m and the maximum height was 18m. Unit weight for each floor was 1.0t/m2. The building natural period was set to 0.36sec, and the initial stiffness of each floor was calculated by assuming the 1st mode to be an inverted triangle. First, we investigated the difference of the dynamic characteristics depending on the difference of initial damping model setting. With the increase in the maximum acceleration of the input earthquake motions, the 1st and 2nd natural frequency decreased, and the 1st damping ratio increased. Then, in the natural frequency, the difference due to initial damping model setting was small, but in the damping ratio, a significant difference was observed (Initial stiffness proportional≒Rayleigh type>Tangent stiffness proportional). The acceleration and the displacement of the earthquake response were largest in the tangent stiffness proportional. In the range where the acceleration response increased, the damping ratio was constant. In the range where the acceleration response was constant, the damping ratio increased. Next, we investigated the difference of the dynamic characteristics depending on the difference of hysteretic model setting. With the increase in the maximum acceleration of the input earthquake motions, the natural frequency decreased in TAKEDA model, but in Normal-trilinear model, the natural frequency didn’t change. The damping ratio in TAKEDA model was higher than that in Normal-trilinear model, although, both in TAKEDA model and Normal-trilinear model, the damping ratio increased. In conclusion, in initial damping model setting, the tangent stiffness proportional was evaluated the most. In the hysteretic model setting, TAKEDA model was more appreciated than the Normal-trilinear model in the nonlinear region. Our results would provide useful indicator on dynamic design.

Keywords: initial damping model, damping ratio, dynamic analysis, hysteretic model, natural frequency

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Authors: Siddhant Sethi, Yasuharu Takashima, Shigetaka Nakamura, Kenzo Fujimoto

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Site-directed mutagenesis is a renowned technique to introduce specific mutations in the genome. To achieve site-directed mutagenesis, many chemical and enzymatic approaches have been reported in the past like disulphite induced genome editing, CRISPR-Cas9, TALEN etc. The chemical methods are invasive whereas the enzymatic approaches are time-consuming and expensive. Most of these techniques are unusable in the cellular application due to their toxicity and other limitations. Photo-chemical cytosine deamination, introduced in 2010, is one of the major technique for enzyme-free single-point mutation of cytosine to uracil in DNA and RNA, wherein, 3-cyanovinylcarbazole nucleoside (CNVK) containing oligodeoxyribonucleotide (ODN) having CNVK at -1 position to that of target cytosine is reversibly crosslinked to target DNA strand using 366 nm and then incubated at 90ºC to accommodate deamination. This technique is superior to enzymatic methods of site-directed mutagenesis but has a disadvantage that it requires the use of high temperature for the deamination step which restricts its applicability in the in vivo applications. This study has been focused on improving the technique by reducing the temperature required for deamination. Firstly, the photo-cross-linker, CNVK has been modified by replacing cyano group attached to vinyl group with methyl ester (OMeVK), amide (NH2VK), and carboxylic acid (OHVK) to observe the acceleration in the deamination of target cytosine cross-linked to vinylcarbazole derivative. Among the derivatives, OHVK has shown 2 times acceleration in deamination reaction as compared to CNVK, while the other two derivatives have shown deceleration towards deamination reaction. The trend of rate of deamination reaction follows the same order as that of hydrophilicity of the vinylcarbazole derivatives. OHVK being most hydrophilic has shown highest acceleration while OMeVK is least hydrophilic has proven to be least active for deamination. Secondly, in the related study, the counter-base of the target cytosine, guanine has been replaced by inosine, 2-aminopurine, nebularine, and 5-nitroindole having distinct hydrogen bonding patterns with target cytosine. Among the ODNs with these counter bases, ODN with inosine has shown 12 fold acceleration towards deamination of cytosine cross-linked to CNVK at physiological conditions as compared to guanosine. Whereas, when 2-aminopurine, nebularine, and 5-nitroindole were used, no deamination reaction took place. It can be concluded that inosine has potential to be used as the counter base of target cytosine for the CNVK mediated photo-cross-linking induced deamination of cytosine. The increase in rate of deamination reaction has been attributed to pattern and number of hydrogen bonding between the cytosine and counter base. One of the important factor is presence of hydrogen bond between exo-cyclic amino group of cytosine and the counter base. These results will be useful for development of more efficient technique for site-directed mutagenesis for C → U transformations in the DNA/RNA which might be used in the living system for treatment of various genetic disorders and genome engineering for making designer and non-native proteins.

Keywords: C to U transformation, DNA editing, genome engineering, ultra-fast photo-cross-linking

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Authors: Ja-Keoung Koo, Kensuke Nakamura, Hyohun Kim, Dongwha Shin, Yeonseok Kim, Ji-Su Ahn, Byung-Woo Hong

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The machine learning techniques based on a convolutional neural network (CNN) have been actively developed and successfully applied to a variety of image analysis tasks including reconstruction, noise reduction, resolution enhancement, segmentation, motion estimation, object recognition. The classical visual information processing that ranges from low level tasks to high level ones has been widely developed in the deep learning framework. It is generally considered as a challenging problem to derive visual interpretation from high dimensional imagery data. A CNN is a class of feed-forward artificial neural network that usually consists of deep layers the connections of which are established by a series of non-linear operations. The CNN architecture is known to be shift invariant due to its shared weights and translation invariance characteristics. However, it is often computationally intractable to optimize the network in particular with a large number of convolution layers due to a large number of unknowns to be optimized with respect to the training set that is generally required to be large enough to effectively generalize the model under consideration. It is also necessary to limit the size of convolution kernels due to the computational expense despite of the recent development of effective parallel processing machinery, which leads to the use of the constantly small size of the convolution kernels throughout the deep CNN architecture. However, it is often desired to consider different scales in the analysis of visual features at different layers in the network. Thus, we propose a CNN model where different sizes of the convolution kernels are applied at each layer based on the random projection. We apply random filters with varying sizes and associate the filter responses with scalar weights that correspond to the standard deviation of the random filters. We are allowed to use large number of random filters with the cost of one scalar unknown for each filter. The computational cost in the back-propagation procedure does not increase with the larger size of the filters even though the additional computational cost is required in the computation of convolution in the feed-forward procedure. The use of random kernels with varying sizes allows to effectively analyze image features at multiple scales leading to a better generalization. The robustness and effectiveness of the proposed CNN based on random kernels are demonstrated by numerical experiments where the quantitative comparison of the well-known CNN architectures and our models that simply replace the convolution kernels with the random filters is performed. The experimental results indicate that our model achieves better performance with less number of unknown weights. The proposed algorithm has a high potential in the application of a variety of visual tasks based on the CNN framework. Acknowledgement—This work was supported by the MISP (Ministry of Science and ICT), Korea, under the National Program for Excellence in SW (20170001000011001) supervised by IITP, and NRF-2014R1A2A1A11051941, NRF2017R1A2B4006023.

Keywords: deep learning, convolutional neural network, random kernel, random projection, dimensionality reduction, object recognition

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Authors: Hyohun Kim, Dongwha Shin, Yeonseok Kim, Ji-Su Ahn, Kensuke Nakamura, Dongeun Choi, Byung-Woo Hong

Abstract:

Artefacts are commonly encountered in the imaging process of clinical computed tomography (CT) where the artefact refers to any systematic discrepancy between the reconstructed observation and the true attenuation coefficient of the object. It is known that CT images are inherently more prone to artefacts due to its image formation process where a large number of independent detectors are involved, and they are assumed to yield consistent measurements. There are a number of different artefact types including noise, beam hardening, scatter, pseudo-enhancement, motion, helical, ring, and metal artefacts, which cause serious difficulties in reading images. Thus, it is desired to remove nuisance factors from the degraded image leaving the fundamental intrinsic information that can provide better interpretation of the anatomical and pathological characteristics. However, it is considered as a difficult task due to the high dimensionality and variability of data to be recovered, which naturally motivates the use of machine learning techniques. We propose an image restoration algorithm based on the deep neural network framework where the denoising auto-encoders are stacked building multiple layers. The denoising auto-encoder is a variant of a classical auto-encoder that takes an input data and maps it to a hidden representation through a deterministic mapping using a non-linear activation function. The latent representation is then mapped back into a reconstruction the size of which is the same as the size of the input data. The reconstruction error can be measured by the traditional squared error assuming the residual follows a normal distribution. In addition to the designed loss function, an effective regularization scheme using residual-driven dropout determined based on the gradient at each layer. The optimal weights are computed by the classical stochastic gradient descent algorithm combined with the back-propagation algorithm. In our algorithm, we initially decompose an input image into its intrinsic representation and the nuisance factors including artefacts based on the classical Total Variation problem that can be efficiently optimized by the convex optimization algorithm such as primal-dual method. The intrinsic forms of the input images are provided to the deep denosing auto-encoders with their original forms in the training phase. In the testing phase, a given image is first decomposed into the intrinsic form and then provided to the trained network to obtain its reconstruction. We apply our algorithm to the restoration of the corrupted CT images by the artefacts. It is shown that our algorithm improves the readability and enhances the anatomical and pathological properties of the object. The quantitative evaluation is performed in terms of the PSNR, and the qualitative evaluation provides significant improvement in reading images despite degrading artefacts. The experimental results indicate the potential of our algorithm as a prior solution to the image interpretation tasks in a variety of medical imaging applications. This work was supported by the MISP(Ministry of Science and ICT), Korea, under the National Program for Excellence in SW (20170001000011001) supervised by the IITP(Institute for Information and Communications Technology Promotion).

Keywords: auto-encoder neural network, CT image artefact, deep learning, intrinsic image representation, noise reduction, total variation

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