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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.
Otokozawa, Seiko,Tanaka, Ryoichi,Akasaka, Hiroshi,Ito, Eiki,Asakura, Sumiyo,Ohnishi, Hirofumi,Saito, Shigeyuki,Miura, Tetsuji,Saito, Tsuyoshi,Mori, Mitsuru Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.12
Background: The aim of this study was to examine the association of serum isoflavones, adiponectin, and insulin levels with ovarian cancer risk. Materials and Methods: We gathered cases with histologically confirmed epithelial ovarian cancer at Sapporo Medical University Hospital from October 2010 to September 2012. Potential controls were recruited from female inpatients without any history of cancer or diabetes mellitus in different wards of the same hospital over the same period of time. Serum isoflavones, adiponectin, and insulin levels were measured in order to estimate associations with ovarian cancer risk in a case-control study. Data from 71 cases and 80 controls were analyzed with a logistic regression model adjusting for known risk factors. Results: A significant reduction in ovarian cancer risk was observed for the high tertile of serum daidzein level versus the low ($P_{trend}<0.001$). A significant reduction in ovarian cancer risk was also observed for the high tertile of serum glycitein level versus the low ($P_{trend}=0.005$). Furthermore, a significant reduction in ovarian cancer risk was observed for the high tertile of serum adiponectin level versus the low ($P_{trend}=0.004$). Conversely, serum insulin level showed significantly elevated risk for ovarian cancer with the high tertile versus the low $P_{trend}<0.001$). Conclusions: Decreased serum isoflavones levels, such as those for daidzein and glycitein, decreased serum adiponectin levels, and increased serum insulin levels could be shown to be associated with elevated risk of ovarian cancer.
Kei Matsumoto,Shinwa Tanaka,Takashi Toyonaga,Nobuaki Ikezawa,Mari Nishio,Masanao Uraoka,Tomoatsu Yoshihara,Hiroya Sakaguchi,Hirofumi Abe,Tetsuya Yoshizaki,Madoka Takao,Toshitatsu Takao,Yoshinori Morit 대한소화기내시경학회 2022 Clinical Endoscopy Vol.55 No.1
Background/Aims: The anastomotic site after distal gastrectomy is the area most affected by duodenogastric reflux. Differentreconstruction methods may affect the lesion characteristics and treatment outcomes of remnant gastric cancers at the anastomoticsite. We retrospectively investigated the clinicopathologic and endoscopic submucosal dissection outcomes of remnant gastriccancers at the anastomotic site. Methods: We recruited 34 consecutive patients who underwent endoscopic submucosal dissection for remnant gastric cancer at theanastomotic site after distal gastrectomy. Clinicopathology and treatment outcomes were compared between the Billroth II and non-Billroth II groups. Results: The tumor size in the Billroth II group was significantly larger than that in the non-Billroth II group (22 vs. 19 mm;p=0.048). More severe gastritis was detected endoscopically in the Billroth II group (2 vs. 1.33; p=0.0075). Moreover, operation timewas longer (238 vs. 121 min; p=0.004) and the frequency of bleeding episodes was higher (7.5 vs. 3.1; p=0.014) in the Billroth IIgroup. Conclusions: Compared to remnant gastric cancers in non-Billroth II patients, those in the Billroth II group had larger lesions with abackground of severe remnant gastritis. Endoscopic submucosal dissection for remnant gastric cancers in Billroth II patients involvedlonger operative times and more frequent bleeding episodes than that in patients without Billroth II.
Jothi Saravanan Thiyagarajan,Di Su,Hirofumi Tanaka,Boyu Zhao,Tomonori Nagayama 국제구조공학회 2021 Smart Structures and Systems, An International Jou Vol.27 No.2
Condition monitoring of railway tracks is essential in guaranteeing the running safety of railways. Track profiles are the primary source of external excitation for a train system. While Track Recording Vehicle is often utilized for maintenance purposes, this particular vehicle is expensive and difficult to use for small railway operators. Therefore, track profile estimation through in-service vehicle response measurements, which potentially provides efficient and frequent measurement, has been studied. However, the quantitative evaluation of the vertical and lateral track profile irregularities is still challenging as the inverse analysis solutions are sometimes inaccurate and even unstable. In this paper, numerical analyses are first carried out to evaluate track profiles from acceleration and angular velocity responses measured on a train car body. For the inverse analysis, an Augmented State Kalman Filter is utilized to solve the problem using 4 degrees of freedom observable train models. The sensor installation locations are investigated through observability rank condition analysis with different measurement layout. Secondly, a field experiment is carried out in a local Japanese in-service railway network to estimate track profile from car body motions. Smartphones are utilized for the field test measurements as prevalent sensing devices. The effectiveness of the proposed approach is demonstrated with the observable train model. Numerical analyses and field experiments clarify the proposed track profile estimation’s capability using only one on-board sensing device.
Nobuaki Ikezawa,Takashi Toyonaga,Shinwa Tanaka,Tetsuya Yoshizaki,Toshitatsu Takao,Hirofumi Abe,Hiroya Sakaguchi,Kazunori Tsuda,Satoshi Urakami,Tatsuya Nakai,Taku Harada,Kou Miura,Takahisa Yamasaki,Stu 대한소화기내시경학회 2022 Clinical Endoscopy Vol.55 No.3
Background/Aims: Endoscopic submucosal dissection (ESD) for diverticulum-associated colorectal lesions is generally contraindicatedbecause of the high risk of perforation. Several studies on patients with such lesions treated with ESD have been reported recently. However, the feasibility and safety of ESD for lesions in proximity to a colonic diverticulum (D-ESD) have not been fully clarified. Theaim of this study was to evaluate the feasibility and safety of D-ESD. Methods: D-ESD was defined as ESD for lesions within approximately 3 mm of a diverticulum. Twenty-six consecutive patients whounderwent D-ESD were included. Two strategic approaches were used depending on whether submucosal dissection of the diverticulum-related part was required (strategy B) or not (strategy A). Treatment outcomes and adverse events associated with each strategywere analyzed. Results: The en bloc resection rate was 96.2%. The R0 and curative resection rates were 76.4% and 70.6% in strategy A and 88.9% and77.8% in strategy B, respectively. Two cases of intraoperative perforation and one case of delayed perforation occurred. The delayed perforationcase required emergency surgery, but the other cases were managed conservatively. Conclusions: D-ESD may be a feasible treatment option. However, it should be performed in a high-volume center by expert handsbecause it requires highly skilled endoscopic techniques.
Hiroyuki Kaji,Akira Togayachi,Makoto Ochou,Maki Sogabe,Takashi Okura,Hirofumi Nozaki,Takashi Angata,Yasunori Chiba,Hidenori Ozaki,Atsushi Kuno,Yasuhito Tanaka,Yuzuru Ikehara,Masashi Mizokami,Hisashi N 한국당과학회 2012 한국당과학회 학술대회 Vol.2012 No.1
We present here a high-throughput strategy to discover serological biomarkers for early-detection of hepatocellular carcinoma (HCC). Our strategy is also applicable to assess the progressed liver fibrosis that is associated with virus hepatitis. The glycan structure on glycoproteins derived from cancerous cells is known to be different from that derived from normal cells, specifically, the increased aberrant glycosylation appears in patient serum with virus hepatitis along with either or both the initiation and progression. Based on the above perceptions, in order to identify glycoproteins carrying aberrant glycosylation in serum of liver disease patients, we analyzed lectin-captured glycopeptides by the IGOT method. Many glycoproteins carrying altered glycans were successfully identified. The increased amount of these glycoproteins was clinically relevant to the progression of the liver diseases. We are now selecting appropriate molecules depending on the feasibility to detect an abnormality in the liver, such as the occurrence of liver cell neoplasm.
Long, Le Ngoc,Thi, Pham Tan,Trung Kien, Pham,Trung, Pham Thanh,Ohtani, Masataka,Kumabe, Yoshitaka,Tanaka, Hirofumi,Ueda, Shigenori,Lee, Hyoyoung,Thang, Phan Bach,Khai, Tran Van Elsevier 2020 APPLIED SURFACE SCIENCE - Vol.504 No.-
<P><B>Abstract</B></P> <P>In this study, a novel hydrothermal route has been developed for the synthesis of MoS<SUB>2</SUB>/graphene composite with controllable structures, in which ammonium molybdatetetrahydrate, as-prepared graphene oxide (GO), and thioacetamide were used as staring materials. Effects of Mo<SUP>4+</SUP>-to-C precursor ratios and crystalline time on the structures, components and morphologies of MoS<SUB>2</SUB>/graphene were investigated. MoS<SUB>2</SUB>/graphene samples were characterized using XRD, FESEM, HRTEM, FTIR, Raman spectroscopy, HAADF-STEM/EDS, HXPES and electrical measurements. The results show that petal-like MoS<SUB>2</SUB> nanostructures with ultrathin petals (~1–10 layers) and coexistence of 1T- and 2H-MoS<SUB>2</SUB> phases can be synthesized on graphene surface in a short time (~2 h). Comparison of crystallization conditions, we found that the crystallization time had a significant effect on the size of the MoS<SUB>2</SUB> nanopetals. The shorter the reaction time is, the thinner the petal-like MoS<SUB>2</SUB> nanoscale is. On the other hand, by adjusting the ratios of Mo<SUP>4+</SUP>to C (denoted as: MoS<SUB>2</SUB>/C (1:2), MoS<SUB>2</SUB>/C (3:2), MoS<SUB>2</SUB>/C (2.5:1) and MoS<SUB>2</SUB>/C (3:1)), different MoS<SUB>2</SUB>/graphene architectures including “sandwich-liked”, “layer–by–layer” and “anchored” can be obtained. On the basis of these results, a possible growth mechanism of MoS<SUB>2</SUB>nanopetals on GO was proposed. Interestingly, the as-synthesized material depicts its memristive behavior through the Volt-Ampere characteristics, suggesting a potential application in logic memory devices.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A novel hydrothermal route has been developed for the synthesis of MoS<SUB>2</SUB>/graphene composite with controllable structures. </LI> <LI> The effects of Mo<SUP>4+</SUP>-to-C precursor ratios and crystalline time on properties of MoS<SUB>2</SUB>/graphene were investigated by FESEM, HRTEM, XRD, FTIR, Raman spectroscopy, HAADF-STEM/EDS and HXPES. </LI> <LI> The memristive properties of the MoS<SUB>2</SUB>/graphenenanocomposite were presented. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>