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Takasawa Ken,Asada Ken,Kaneko Syuzo,Shiraishi Kouya,Machino Hidenori,Takahashi Satoshi,Shinkai Norio,Kouno Nobuji,Kobayashi Kazuma,Komatsu Masaaki,Mizuno Takaaki,Okubo Yu,Mukai Masami,Yoshida Tatsuya 생화학분자생물학회 2024 Experimental and molecular medicine Vol.56 No.-
DNA methylation is an epigenetic modification that results in dynamic changes during ontogenesis and cell differentiation. DNA methylation patterns regulate gene expression and have been widely researched. While tools for DNA methylation analysis have been developed, most of them have focused on intergroup comparative analysis within a dataset; therefore, it is difficult to conduct cross-dataset studies, such as rare disease studies or cross-institutional studies. This study describes a novel method for DNA methylation analysis, namely, methPLIER, which enables interdataset comparative analyses. methPLIER combines Pathway Level Information Extractor (PLIER), which is a non-negative matrix factorization (NMF) method, with regularization by a knowledge matrix and transfer learning. methPLIER can be used to perform intersample and interdataset comparative analysis based on latent feature matrices, which are obtained via matrix factorization of large-scale data, and factor-loading matrices, which are obtained through matrix factorization of the data to be analyzed. We used methPLIER to analyze a lung cancer dataset and confirmed that the data decomposition reflected sample characteristics for recurrence-free survival. Moreover, methPLIER can analyze data obtained via different preprocessing methods, thereby reducing distributional bias among datasets due to preprocessing. Furthermore, methPLIER can be employed for comparative analyses of methylation data obtained from different platforms, thereby reducing bias in data distribution due to platform differences. methPLIER is expected to facilitate cross-sectional DNA methylation data analysis and enhance DNA methylation data resources.
Kobayashi, Masayuki,Masaoka, Shigeyuki,Sakai, Ken Korean Society of Photoscience 2009 Photochemical & photobiological sciences Vol.8 No.2
A water-soluble ortho-metalated platinum(II) complex $[K(18-crown-6)][Pt(ppy)Cl_2]{\cdot}5H_2O$ (1) (ppy = phenylpyridinate, 18-crown-6 = 1,4,7,10,13,16-hexaoxacyclooctadecane) was prepared from a 1 : 1 reaction of $[K(18-crown-6)]_2[PtCl_4]$ and 2-phenylpyridine in methanol. The compound crystallizes in the triclinic system, space group $P{\bar{1}$ (No. 2). A solvolysis product of 1, Pt(ppy)Cl(DMF) (DMF = N,N-dimethylformamide) (10), was also isolated and structurally characterized by X-ray diffraction (monoclinic system, space group $P2_1$/n (No. 14)), revealing the lability of the coordination bond trans to the C(ppy) donor. Ligand substitution reactions of 1 in water were investigated by means of UV-visible absorption spectroscopy and time-dependent DFT calculations. The initial hydrolysis product in aqueous media was suggested to be Pt(ppy)Cl($OH_2$), in which the chloride ion trans to the C(ppy) donor in $[Pt(ppy)Cl_2]^-$ is replaced with an aqua ligand due to the stronger trans effect originated by the C(ppy) donor. It was found that the ligand substitution reactions of $[Pt(ppy)Cl_2]^-$ is extremely complicated. Leaving the complex in solution for a prolonged time resulted in deposition of a yellowish green chloride-bridged dimer $Pt_2(ppy)_2({\mu}-Cl)_2$. Moreover, an unidentified blue species, ascribable to a Pt(II)/Pt(III) mixed-valence species, started to form while the initial hydrolysis reactions proceeded. Photochemical hydrogen production from water catalyzed by $[Pt(ppy)Cl_2]^-$ was examined using a photosystem made up of ${Ru(bpy)3}^{2+}$ (bpy = 2,2'-bipyridine), methylviologen, and a sacrificial electron donor (EDTA) in an acetate buffer (pH 5). It is shown that the $H_2$-evolving activity of $[Pt(ppy)Cl_2]^-$ is higher that those of the hydrolysis products of $[Pt(ppy)Cl_2]^-$, but are comparable to those of other common Pt(II) complexes having a cis-Pt(II)$Cl_2$ unit, such as cis-$PtCl_2(NH_3)_2$, $PtCl_2$(4,4'-dicarboxybpy), and $PtCl_2$(2,2'-bipyrimidine).
A Multiobjective Model for Locating Drop-off Boxes for Collecting Used Products
Ken-ichi Tanaka,Hirokazu Kobayashi,Kenji Yura 대한산업공학회 2013 Industrial Engineeering & Management Systems Vol.12 No.4
This paper proposes a multiobjective model describing the trade-offs involved in selecting the locations of drop-off boxes for collecting used products and transporting these products to designated locations. We assume the following reverse flow of used products. Owners of used products (cellular phones, digital cameras, ink cartridges, etc.) take them to the nearest drop-off box when the distance is reasonably short. We also assume that owners living closer to drop-off boxes dispose of more used products than do owners living farther from drop-off boxes. Different types of used products are collected, with each type requiring its own drop-off box. A transportation destination for each product is specified. Three objectives are considered: maximizing the volume of used products collected at drop-off boxes; minimizing the cost of transporting collected products to designated locations; and minimizing the cost of allocating space for drop-off boxes. We formulate the above model as a multiobjective integer programming problem and generate the corresponding set of Pareto optimal solutions. We apply the model to an area using population data for Chofu City, Tokyo, Japan, and analyze the trade-offs between the objectives.
Archetype Model-Driven Development Framework for EHR Web System
Shinji Kobayashi,Eizen Kimura,Ken Ishihara 대한의료정보학회 2013 Healthcare Informatics Research Vol.19 No.4
Objectives: This article describes the Web application framework for Electronic Health Records (EHRs) we have developed to reduce construction costs for EHR sytems. Methods: The openEHR project has developed clinical model driven architecture for future-proof interoperable EHR systems. This project provides the specifications to standardize clinical domain model implementations, upon which the ISO/CEN 13606 standards are based. The reference implementation has been formally described in Eiffel. Moreover C# and Java implementations have been developed as reference. While scripting languages had been more popular because of their higher efficiency and faster development in recent years, they had not been involved in the openEHR implementations. From 2007, we have used the Ruby language and Ruby on Rails (RoR) as an agile development platform to implement EHR systems, which is in conformity with the openEHR specifications. Results: We implemented almost all of the specifications, the Archetype Definition Language parser, and RoR scaffold generator from archetype. Although some problems have emerged, most of them have been resolved. Conclusions: We have provided an agile EHR Web framework, which can build up Web systems from archetype models using RoR. The feasibility of the archetype model to provide semantic interoperability of EHRs has been demonstrated and we have verified that that it is suitable for the construction of EHR systems.
Clinicopathological Significance of S100A10 Expression in Lung Adenocarcinomas
Katono, Ken,Sato, Yuichi,Jiang, Shi-Xu,Kobayashi, Makoto,Saito, Keita,Nagashio, Ryo,Ryuge, Shinichiro,Satoh, Yukitoshi,Saegusa, Makoto,Masuda, Noriyuki Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.1
Background: S100A10, of the S100 protein family, is reported to be involved in cancer cell invasion and metastasis. The aims of the present study were to immunohistochemically examine S100A10 expression in surgically resected lung adenocarcinomas, and evaluate any relationships with clinicopathological parameters and prognosis of patients. Materials and Methods: S100A10 expression was immunohistochemically studied in 202 consecutive resected lung adenocarcinomas, and its associations with clinicopathological parameters were evaluated. Kaplan-Meier survival analysis and Cox proportional hazards models were used to estimate the effect of S100A10 expression on survival. Results: S100A10 expression was detected in 65 of the 202 (32.2%) lung adenocarcinomas, being significantly correlated with poorer differentiation (P =0.015), a higher pathological TNM stage (stages II and III) (P=0.004), more frequent and severe intratumoral vascular invasion (P=0.001), and a poorer prognosis (P=0.030). However, S100A10 expression was not an independent predictor of survival after controlling for clinicopathological factors. Conclusions: The present study reveals that S100A10 is expressed in a subset of lung adenocarcinomas, and this is related to some clinicopathological parameters, although further studies are required to confirm the correlation between S100A10 expression and prognosis of lung adenocarcinoma patients.
Ogura, Ichiro,Kobayashi, Eizaburo,Nakahara, Ken,Haga-Tsujimura, Maiko,Igarashi, Kensuke,Katsumata, Akitoshi Korean Academy of Oral and Maxillofacial Radiology 2019 Imaging Science in Dentistry Vol.49 No.4
Purpose: The purpose of this study was to evaluate the morphology of the mandibular cortex in cases of medication-related osteonecrosis of the jaw (MRONJ) in patients with osteoporosis or bone metastases using a computer programme. Materials and Methods: Fifty-four patients with MRONJ (35 with osteoporosis and 19 with bone metastases) were examined using panoramic radiography. The morphology of the mandibular cortex was evaluated using a computer programme that scanned the mandibular inferior cortex and automatically assessed the mandibular cortical index (MCI) according to the thickness and roughness of the mandibular cortex, as follows: normal (class 1), mildly to moderately eroded (class 2), or severely eroded (class 3). The MCI classifications of MRONJ patients with osteoporosis or bone metastases were evaluated with the Pearson chi-square test. In these analyses, a 5% significance level was used. Results: The MCI of MRONJ patients with osteoporosis(class 1: 6, class 2: 15, class 3: 14) tended to be higher than that of patients with bone metastases(class 1: 14, class 2: 5, class 3: 0)(P=0.000). Conclusion: The use of a computer programme to assess mandibular cortex morphology may be an effective technique for the objective and quantitative evaluation of the MCI in MRONJ patients with osteoporosis or bone metastases.
Satoshi Sugino,Ken Inoue,Reo Kobayashi,Ryohei Hirose,Toshifumi Doi,Akihito Harusato,Osamu Dohi,Naohisa Yoshida,Kazuhiko Uchiyama,Takeshi Ishikawa,Tomohisa Takagi,Hiroaki Yasuda,Hideyuki Konishi,Yasuko 대한소화기 기능성질환∙운동학회 2022 Journal of Neurogastroenterology and Motility (JNM Vol.28 No.4
Background/Aims Several studies have assessed the effect of cool temperature on colonic peristalsis. Transient receptor potential melastatin 8 (TRPM8) is a temperature-sensitive ion channel activated by mild cooling expressed in the colon. We examined the antispasmodic effect of cool temperature on colonic peristalsis in a prospective, randomized, single-blind trial and based on the video imaging and intraluminal pressure of the proximal colon in rats and TRPM8-deficient mice. Methods In the clinical trial, we randomly assigned a total of 94 patients scheduled to undergo colonoscopy to 2 groups: the mildly cool water (n = 47) and control (n = 47) groups. We used 20 mL of 15°C water for the mildly cool water. The primary outcome was the proportion of subjects with improved peristalsis after treatment. In the rodent proximal colon, we evaluated the intraluminal pressure and performed video imaging of the rodent proximal colon with cool water administration into the colonic lumen. Clinical trial registry website (Trial No. UMIN-CTR; UMIN000030725). Results In the randomized controlled trial, after treatment, the proportion of subjects with no peristalsis with cool water was significantly higher than that in the placebo group (44.7% vs 23.4%; P < 0.05). In the rodent colon model, cool temperature water was associated with a significant decrease in colonic peristalsis through its suppression of the ratio of peak frequency (P < 0.05). Cool temperature-treated TRPM8-deficient mice did not show a reduction in colonic peristalsis compared with wild-type mice. Conclusion For the first time, this study demonstrates that cool temperature-dependent suppression of colonic peristalsis may be associated with TRPM8 activation.