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Fragment Molecular Orbital Method: Application to Protein-Ligand Binding
Watanabe, Hirofumi,Tanaka, Shigenori Korean Society for Bioinformatics 2010 Interdisciplinary Bio Central (IBC) Vol.2 No.2
Fragment molecular orbital (FMO) method provides a novel tool for ab initio calculations of large biomolecules. This method overcomes the size limitation difficulties in conventional molecular orbital methods and has several advantages compared to classical force field approaches. While there are many features in this method, we here focus on explaining the issues related to protein-ligand binding: FMO method provides useful interaction-analysis tools such as IFIE, CAFI and FILM. FMO calculations can provide not only binding energies, which are well correlated with experimental binding affinity, but also QSAR descriptors. In addition, FMO-derived charges improve the descriptions of electrostatic properties and the correlations between docking scores and experimental binding affinities. These calculations can be performed by the ABINIT-MPX program and the calculation results can be visualized by its proper BioStation Viewer. The acceleration of FMO calculations on various computer facilities is ongoing, and we are also developing methods to deal with cytochrome P450, which belongs to the family of drug metabolic enzymes.
Present State and Future Trends of Active Power Filters in Japan
Hirofumi Akagi,Noriyuki Watanabe 전력전자학회 1992 ICPE(ISPE)논문집 Vol.1992 No.4
With remarkable development and advance in PWM inverter technology on the basis of fast switching devices in the 1980s, active power filters which are classified into shunt and series active filters have been studied with the focus on their practical installation in industrial power systems. In 1982, a shunt active filter of rating 800kVA was put into practical use for the first time in the world. The main circuit consisted of a current source PWM inverter using GTO thyristors. In 1986, a combined system of a shunt active filter of rating 900kVA and a shunt passive filter of rating 6600kVA was practically installed to suppress the harmonics produced by a large capacity cycloconverter for steel mill drives.<br/> More than one hundred shunt active filters have been operating properly in Japan. The largest one of the shunt active filters is 20MVA, which was developed in 1990 for reactive power and harmonic compensation for an arc furnace with the help of a shunt passive filter of 20MVA.<br/> This paper presents a survey of shunt and series active filters using PWM inverters, paying attention to research and practical applications in Japan.<br/>
Unstructured Information Management Projects at IBM Tokyo Research Laboratory
Takeda, Koichi,Watanabe, Hideo,Uramoto, Naohiko,Nomiyama, Hiroshi,Matsuzawa, Hirofumi,Nasukawa, Tetsuya,Nagano, Tohru,Murakami, Akiko,Takeuchi, Hironori,Kanayama, Hiroshi,Kobayashi, Mei,Aono, Masaki,I 한국정보처리학회 2004 정보처리학회지 Vol.11 No.2
In-grid Demonstration of High-temperature Superconducting Cable
Ohya, Masayoshi,Ashibe, Yuichi,Watanabe, Michihiko,Yumura, Hiroyasu,Nakanishi, Tatsuo,Hirota, Hirofumi,Masuda, Takato,Ichikawa, Hiroshi,Mimura, Tomoo,Honjo, Shoichi,Hara, Tsukushi The Korean Institute of Electrical Engineers 2013 The Journal of International Council on Electrical Vol.3 No.2
In a national project that began in 2007, Tokyo Electric Power Company (TEPCO), Sumitomo Electric Industries (SEI) and Mayekawa Mfg. Corporation (MYCOM) aim to operate a 66 kV, 200 MVA HTS cable system in a power grid to demonstrate its reliability and stable operation. In order to verify the validity of the cable design, a 30 m HTS cable system was constructed and subjected to various tests. After the confirmation of the nominal current and voltage performance, a long-term operation test was performed to verify whether the HTS cable system is capable of handling the rated current and voltage for thirty years. A 250 m cable was manufactured for the in-grid demonstration, and shipping tests were successful. The cable system construction was completed at the Asahi substation (Yokohama, Kanagawa), and the in-grid demonstration will start in 2012.
( Teppei Komiya ),( Takuma Maeda ),( Yuki Kajino ),( Hirofumi Nakayama ),( Takayuki Shimaoka ),( Takayuki Hirao ),( Shuji Watanabe ),( Makoto Takemoto ),( Naoya Maeda ),( Akiyuki Ukai ),( Fumihiro Kas 한국폐기물자원순환학회(구 한국폐기물학회) 2019 한국폐기물자원순환학회 심포지움 Vol.2019 No.1
Approximately 20% of solid waste in Japan is disposed of at coastal landfill sites. It is an issue that it takes long-term to stabilize coastal landfill sites. Municipal solid waste incineration bottom ash (BA) is one of main wastes landfilled at coastal landfill sites. It is known that finer particles contain more contaminants in BA1), and it was demonstrated that the removal of finer particles from BA produced the lowering pH of leachate as well as the increase of permeability of the landfilled waste layer2). In this study, open channel (OC) classification was focused on as a feasible technique to remove finer particles from BA on a coastal landfill site, and its demonstrational experiment was carried out in order to clarify if the fine particle fraction (d<0.425mm) (FPF) could be removed from BA by OC classification and the settling characteristics of BA in OC. Fig. 1 shows the experimental apparatus. The sea water in a coastal landfill site was pumped up and flowed in OC, and BA is supplied on the surface of the flowing water. After completions of the settling and outflow of BA, saucers on the bottom of OC was collected, and the dry weight and particle size distribution of the BA sediment in each saucer were measured. Table 1 shows the experimental condition. The settling section means the part of OC from the BA supply point to the end of OC. Fig. 2 shows the removal ratio of FPF by OC classification, which is the ratio of the dry weight of FPF in the BA sediment to that in the BA supplied. The largest removal ratio was 61% in Case 3 with the largest water flow velocity and the shortest length of settling section. Fig. 3 shows the median of the settling velocity of BA in OC (MSV) compared with the theoretical settling velocity by Allen’s and Newton’s laws (TSV). The MSV of BA particles greater than 3mm was almost 50% of TSV, and MSV became closer to TSV as BA’s particle size became smaller. The MSV of BA particles with a diameter of 0.425mm was approximately 80% of TSV.
Novel mutations of CDKN1C in Japanese patients with Beckwith-Wiedemann syndrome
Hitomi Yatsuki,Ken Higashimoto,Kosuke Jozaki,Kayoko Koide,Junichiro Okada,Yoriko Watanabe,Nobuhiko Okamoto,Yoshinobu Tsuno,Yoko Yoshida,Kazutoshi Ueda,Kenji Shimizu,Hirofumi Ohashi,Tsunehiro Mukai,Hid 한국유전학회 2013 Genes & Genomics Vol.35 No.2
Beckwith-Wiedemann syndrome (BWS) is an imprinting-related human disease that is characterized by macrosomia, macroglossia, abdominal wall defects, and variable minor features. BWS is caused by several genetic/epigenetic alterations, such as loss of methylation at KvDMR1,gain of methylation at H19-DMR, paternal uniparental disomy of chromosome 11, CDKN1C mutations, and structural abnormalities of chromosome 11. CDKN1C is an imprinted gene with maternal preferential expression, encoding for a cyclin-dependent kinase (CDK) inhibitor. Mutations in CDKN1C are found in 40 % of familial BWS cases with dominant maternal transmission and in *5 % of sporadic cases. In this study, we searched for CDKN1C mutations in 37BWS cases that had no evidence for other alterations. We found five mutations—four novel and one known—from a total of six patients. Four were maternally inherited and one was a de novo mutation. Two frame-shift mutations and one nonsense mutation abolished the QT domain, containing a PCNA-binding domain and a nuclear localization signal. Two missense mutations occurred in the CDK inhibitory domain,diminishing its inhibitory function. The above-mentioned mutations were predicted by in silico analysis to lead to loss of function; therefore, we strongly suspect that such anomalies are causative in the etiology of BWS.
Association between periodontal bacteria and degenerative aortic stenosis: a pilot study
Kataoka, Akihisa,Katagiri, Sayaka,Kawashima, Hideyuki,Nagura, Fukuko,Nara, Yugo,Hioki, Hirofumi,Nakashima, Makoto,Sasaki, Naoki,Hatasa, Masahiro,Maekawa, Shogo,Ohsugi, Yujin,Shiba, Takahiko,Watanabe, Korean Academy of Periodontology 2021 Journal of Periodontal & Implant Science Vol.51 No.4
Purpose: Although several reports have described the relationship between periodontal disease and cardiovascular disease, information about the association between periodontal disease and the progression of degenerative aortic stenosis (AS) is lacking. Therefore, we performed a retrospective, single-center, pilot study to provide insight into this potential association. Methods: Data from 45 consecutive patients (19 men; median age, 83 years) with mild or moderate degenerative aortic stenosis were analyzed for a mean observation period of 3.3±1.9 years. The total amount of Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis and titers of serum immunoglobulin G (IgG) against periodontal bacteria and high-sensitivity C-reactive protein (hs-CRP) were evaluated. Aortic valve area (AVA), maximal velocity (Vmax), mean pressure gradient (mean PG), and the Doppler velocity index (DVI) were evaluated. The change in each parameter per year ([Parameter<sub>LATEST</sub>-Parameter<sub>BASELINE</sub>]/Follow-up Years) was calculated from the retrospective follow-up echocardiographic data (baseline vs. the most recently collected data [latest]). Results: No correlation was found between the concentration of periodontopathic bacteria in the saliva and AS status/progression. The anti-P. gingivalis antibody titer in the serum showed a significant positive correlation with AVA and DVI. Additionally, there was a negative correlation between the anti-P. gingivalis IgG antibody titer and mean PG. The hs-CRP concentration showed positive correlations with Vmax and mean PG. Meanwhile, a negative correlation was observed between the anti-P. gingivalis IgG antibody titer and ΔAVA/year and Δmean PG/year. The hs-CRP concentration showed positive correlations with Vmax and mean PG, and it was significantly higher in patients with rapid aortic stenosis progression (ΔAVA/year <-0.1) than in their counterparts. Conclusions: Our results suggest that periodontopathic bacteria such as A. actinomycetemcomitans and P. gingivalis are not directly related to the status/progression of degenerative AS. However, inflammation and a lower immune response may be associated with disease progression.