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Restauro-G:A Rapid Genome Re-Annotation System for Comparative Genomics

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Genomics, Proteomics & Bioinformatics 2007年第1期5卷 53-58页

作者： Satoshi Tamaki Kazuharu Arakawa Nobuaki Kono masaru Tomita Institute for Advanced Biosciences Keio University Fujisawa 252-8520 Japan Department of Environ-mental Information Keio University Fujisawa 252-8520 Japan Institute for Advanced Biosciences Keio University Fujisawa 252-8520 Japan

of complete genome sequences submitted directly from sequencing projects are diverse in terms of annotation strategies and update frequencies. These inconsistencies make comparative studies difficult. To allow rapid data preparation of a large number of complete genomes, automation and speed are important for genome re-annotation. Here we introduce an open-source rapid genome re-annotation software system, Restauro-G, specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLASTLike Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases. Restauro-G was developed in the generic bioinformatics workbench G-language Genome Analysis Environment and is distributed at http：//***/ under the GNU General Public License.

关键词： bioinformatics software annotation G-language Genome Analysis Environment complete genomes

Evaluation of pharmaceutical activities of G-protein coupled receptor targeted pharmaceuticals in Chinese wastewater effluent

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Chinese Chemical Letters 2020年第10期31卷 2859-2863页

作者： Han Zhang Yingchao Lin Zhengyu Men masaru Ihara Weizun Li Kai He College of Environmental Science and Engineering Nankai UniversityTianjin 300071China Research Center for Environmental Quality Management Kyoto UniversityOtsu 5200811Japan

The occurre nce of biologically active pharmaceuticals in aquatic enviro nments raised the potential risks to aquatic *** these marketed biological active pharmaceuticals,it has been estimated that40%of them target G-protein-coupled receptors(GPCRs).We have illustrated pharmaceutical activities of GPCR targeted pharmaceuticals in English and Japanese wastewater by the in vitro transforming growth factor-α(TGFα)shedding ***,as the most important producer and consumer of pharmaceuticals,the occurrence of GPCR targeted pharmaceuticals in China had remained *** this study,we investigated the pharmaceutical activities of GPCR targeted pharmaceuticals in secondary effluents of Chinese wastewater treatment *** discovered antagonistic activities against angiotensin(AT1)receptor at up to 7.2×102 ng-valsartan-equivalent quantity/L in Chinese wastewater for the first time as well as agonistic activities against dopamine(D2)***,in parallel with the assay,we determined concentrations of GPCR targeted pharmaceuticals in target wastewater by liquid chromatography coupled with tandem mass spectrometry(LC-MS/MS).Through the comparison of predicted antagonistic activities calculated by concentrations and potency values from the assay,we found that the measured antagonistic activities against AT1 receptor from the assay were higher than the predicted AT1 activities from valsartan,irbesartan,and losartan,indicating the potential existence of other unknown AT1 antagonists in wastewater.

关键词： PCR targeted pharmaceutical Pharmaceutical activity TGFαshedding assay Wastewater

Lactogenic hormones alter cellular and extracellular microRNA expression in bovine mammary epithelial cell culture

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Journal of Animal Science and Biotechnology 2016年第4期7卷 504-513页

作者： Susumu Muroya Tatsuro Hagi Ataru Kimura Hisashi Aso Masatoshi Matsuzaki masaru Nomura Animal Products Research Division NARO Institute of Livestock and Grassland Science Faculty of Agriculture and Life Science Hirosaki University International Education and Research Center for Food and Agricultural Immunology(CFAI) Graduate School of Agricultural ScienceTohoku University

Background： Bovine milk contains not only a variety of nutritional ingredients but also microRNAs （miRNAs） that are thought to be secreted by the bovine mammary epithelial cells （BMECs）. The objective of this study was to elucidate the production of milk-related miRNAs in BMECs under the influence of lactogenic hormones. Results： According to a microarray result of milk exosomal miRNAs prior to cellular analyses, a total of 257 miRNAs were detected in a Holstein cow milk. Of these, 18 major miRNAs of interest in the milk were selected for an expression analysis in BMEC culture that was treated with or without dexamethasone, insulin, and prolactin （DIP） to induce a lactogenic differentiation. Quantitative polymerase chain reaction （qPCR） results showed that the expressions of miR-21-Sp （P = 0.005）, miR-26a （P = 0.016）, and miR-320a （P = 0.011） were lower in the DIP-treated cells than in the untreated cells. In contrast, the expression of miR-339a （P-- 0.017） in the cell culture medium were lower in the DiP-treated culture than in the untreated culture. Intriguingly, the miR-148a expression in cell culture medium was elevated by DIP treatment of BMEC culture （P = 0.018）. The medium-to-cell expression ratios of miR- 103 （P = 0.025）, miR-148a （P 〈 0.001）, and miR-223 （P = 0.013） were elevated in the DIP-treated BMECs, suggesting that the lactogenic differentiation-induced secretion of these three miRNAs in BMECs. A bioinformatic analysis showed that the miRNAs down-regulated in the BMECs were associated with the suppression of genes related to transcriptional regulation, protein phosphorylation, and tube development. Conclusion： The results suggest that the miRNAs changed by lactogenic hormones are associated with milk protein synthesis, and mammary gland development and maturation. The elevated miR-148a level in DIP-treated BMECs may be associated with its increase in milk during the lactation period of cows.

关键词： Bovine mammary epithelial cell Lactogenic differentiation microRNA Milk Secretion

Investigation and prediction of enteral nutrition problems after percutaneous endoscopic gastrostomy

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World Journal of Gastroenterology 2009年第11期15卷 1367-1372页

作者： Shiro Yokohama masaru Aoshima Yukiomi Nakade Junya Shindo Junichi Maruyama Masashi Yoneda Department of Gastroenterology Asahikawa Rehabilitation HospitalAsahikawa078-8801Japan Division of Gastro-enterology Department of Internal MedicineAichi Medical University School of MedicineAichi 480-1195Japan Department of Rehabilitation Asahikawa Rehabilitation HospitalAsahikawa 078-8801Japan Department of Internal Medicine Asahikawa Rehabilitation HospitalAsahikawa 078-8801Japan

AIM:To investigate and predict enteral nutrition problems after percutaneous endoscopic gastrostomy (PEG). METHODS:We retrospectively analyzed data for 252 out of 285 patients who underwent PEG at our hospital from 1999 to *** nutrition problems after PEG were defined as:(1)patients who required ≥1 mo after surgery to switch to complete enteral nutrition,or who required additional parenteral alimentation continuously;or(2)patients who abandoned switching to enteral nutrition using the gastrostoma and employed other nutritional methods. We attempted to identify the predictors of problem cases by using a logistic regression analysis that examined the patients’backgrounds and the specific causes that led to their problems. RESULTS:Mean age of the patients was 75 years,and in general,their body weight was low and their overall condition was markedly *** testing revealed that patients tended to be anemic and malnourished.A total of 44 patients(17.5%)were diagnosed as having enteral nutrition problems after *** causes ofthe problems included pneumonia,acute enterocolitis (often Clostridium difficile-related),paralytic ileus and biliary tract infection.A multivariate analysis identified the following independent predictors for problem cases:(1)enteral nutrition before gastrectomy(a risk reduction factor);(2)presence of esophageal hiatal hernia;(3)past history of paralytic ileus;and(4) presence of chronic renal dysfunction. CONCLUSION:Enteral nutrition problems after PEG occurred at a comparatively high *** background analysis elucidated four predictive factors for the problem cases.

关键词：经皮内镜下胃造瘘术全肠内营养营养问题预测因素 Logistic回归分析麻痹性肠梗阻慢性肾功能不全聚乙二醇

Electronic transmission of three-terminal pyrene molecular bridge

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Chinese Physics B 2009年第2期18卷 501-505页

作者：王利光张秀梅 Terence Kin Shun Wong Katsunori Tagami masaru Tsukada School of Science Jiangnan University School of Electrical and Electronic Engineering Nanyang Technological University Nano Technology Research Centre Waseda University

This paper investigates theoretically the electronic transmission spectra of the three terminal pyrene molecular bridge and the quantum current distribution on each bond by the tight-binding model based on nonequilibrium Green＇s function and the quantum current density approach, in which one π molecular orbital is taken into account per carbon atom when the energy levels and HOMO-LUMO gap are obtained. The transmission spectra show that the electronic transmission of the three terminal pyrene molecular bridge depends obviously on the incident electronic energy and the pyrene eigenenergy. The symmetrical and oscillation properties of the transmission spectra are illustrated. A novel plus-minus energy switching function is found. The quantum current distribution shows that the loop currents inside the pyrene are induced, and some bond currents are much larger than the input and the output currents. The reasons why the loop currents and the larger bond currents are induced are the phase difference of the atomic orbits and the degeneracy of the molecular orbits. The calculations illustrate that the quantum current distributions are in good agreement with Kirchhoff quantum current conservation law.

关键词： pyrene three terminals electronic transmission current distribution

Current treatment strategies and future perspectives for gastrointestinal stromal tumors

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World Journal of Gastrointestinal Pathophysiology 2022年第1期13卷 15-33页

作者： Yoichi Sugiyama masaru Sasaki Mohei Kouyama Tatsuya Tazaki Shinya Takahashi Atsushi Nakamitsu Department of Gastrointestinal Surgery JA Hiroshima General HospitalHatsukaichi 738-8503HiroshimaJapan Department of Surgery Institute of Biomedical and Health SciencesHiroshima UniversityHiroshima 734-8551Japan

Gastrointestinal stromal tumors(GISTs)are mesenchymal tumors that originate from the gastrointestinal tract,mostly from the *** are derived from the myenteric interstitial cells of Cajal and are caused by several mutations in the c-kit and platelet-derived growth factor receptor ***,GISTs are detected by endoscopic and imaging findings and are diagnosed by *** is the first line of treatment,and if the tumor is relatively small,minimally invasive surgery such as laparoscopy is *** recent years,neoadjuvant therapy has been administered to patients with GISTs that are suspected of having a large size or infiltration to other *** adjuvant imatinib is the standard therapy for high-risk *** is important to assess the risk of recurrence after GIST ***,the effect of tyrosine kinase inhibitor use will vary by the mutation of c-kit genes and the site of ***,information regarding gene mutation is indispensable when considering the treatment policy for recurrent *** article reviews the clinicopathological characteristics of GISTs along with the minimally invasive and multidisciplinary treatment options available for these *** future perspectives for diagnostic and treatment approaches for these tumors have also been discussed.

关键词： Gastrointestinal stromal tumor Minimally invasive surgery Laparoscopic surgery Imatinib Neoadjuvant therapy Risk assessment

Performances of glaucoma operations with Kahook Dual Blade or iStent combined with phacoemulsification in Japanese open angle glaucoma patients

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International Journal of Ophthalmology(English edition) 2020年第6期13卷 941-945页

作者： Kentaro Iwasaki Yoshihiro Takamura Yusuke Orii Shogo Arimura masaru Inatani Department of Ophthalmology Faculty of Medical SciencesUniversity of FukuiFukui 910-1193Japan Department of Ophthalmology Obama HospitalFukui 917-8567Japan

AIM:To compare surgical outcomes of phacoemulsification combined with glaucoma surgical techniques performed with either Kahook Dual Blade(KDB)or iStent for Japanese patients with either primary open angle glaucoma or exfoliation ***:We retrospectively evaluated the surgical outcomes of 129 eyes of 84 Japanese patients with glaucoma who underwent KDB or 44 eyes of 34 patients who underwent phacoemulsification with iStent procedures combined with cataract *** primary outcome was surgical success or failure[with surgical failure being indicated by18 mm Hg as criterion A;IOP>14 mm Hg as criterion B on two consecutive study visits;or reoperation requirement].In addition,we assessed the number of postoperative glaucoma medications and the resulting ***:The probability of success was significantly higher in the KDB group than in the iStent group for criterion A(60.2%vs 46.4%,P=0.019).In the KDB group,the mean preoperative IOP of 19.8±7.3 mm Hg decreased significantly to 13.0±3.1 mm Hg(P<0.01),and the mean number of glaucoma medications at 2.5±1.4 decreased significantly to 1.6±1.6(P<0.01)12 mo *** the iStent group,the mean preoperative IOP of 17.8±2.9 mm Hg significantly decreased to 14.3±2.3 mm Hg(P<0.01),and the mean number of glaucoma medications at 2.2±1.1 decreased significantly to 0.9±1.4(P<0.01)12 mo *** overall IOP reduction percentage was higher in the KDB group(26.2%)than in the iStent group(19.0%)12 mo postoperatively(P=0.03).Hyphema occurred significantly more frequently in the KDB group(16.3%)than in the iStent group(2.3%,P=0.017).CONCLUSION:KDB and iStent procedures combined with cataract surgery both result in significant IOP and glaucoma medication reductions after the 12-month *** patients in the KDB group have a higher success rate for the target IOP of less than 18 mm Hg and a higher complication rate than those

关键词： glaucoma surgery surgical outcome Kahook Dual Blade iStent

SELECTIVE FORMATION OF OXYGENATED COMPOUNDS BY SILICA-SUPPORTED Ru-Co BIMETALLIC CLUSTER-DERIVED CATALYSTS IN CO HYDROGENATION

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Chinese Science Bulletin 1992年第4期37卷 347-348页

作者：肖丰收郭燮贤 ICHIKAWA masaru Department of Chemistry Jilin University Changchun 130023 PRC Dalian Institute of Chemical Physics Academia Sinica Dalian 116023 PRC Catalysis Research Center Hokkaido University Sapporo 060 Japan

It is well known that catalysts prepared from organometallic compounds exhibit high activity and selectivity for oxygenates in CO-based reactions such as CO hydrogenation and olefin hydroformylation, in contrast to the conventional metal catalysts from the usual way of the metal salts. It is also reported that bimetallic catalysts provide quite different

关键词： hydrogenation selectivity salts olefin usual alcohols silica carbonyl aldehyde molar

Case of pseudo-Meigs' syndrome caused by gastric cancer-related metastatic ovarian tumor with prolonged survival

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World Journal of Gastrointestinal Oncology 2016年第11期8卷 801-804页

作者： masaru Okamoto Kazunori Maeda Atsushi Yanagitani Kiwamu Tanaka Department of General Internal Medicine Tottori Prefectural Central Hospital Department of Gastroenterology Tottori Prefectural Central Hospital

A 48-year-old woman presented with bilateral enlarged ovaries, ascites, bilateral pleural effusion, and advanced gastric cancer. Pleural fluid cytology did not reveal malignant cells. Oophorectomy, performed as a palliative procedure, was followed by rapid resolution of the pleural effusion and ascites. The patient was diagnosed with pseudo-Meigs' syndrome, and underwent chemotherapy followed by partial gastrectomy. At the last follow-up, 84 mo following oophorectomy, she was alive, and free of disease recurrence, despite not receiving any further treatment. Pseudo-Meigs' syndrome should be considered in patients with bilateral ovarian tumors, ascites and pleural effusion, and treatment such as oophorectomy may result in symptomatic improvement and better prognosis in similar patients.

关键词： Pseudo-Meigs&rsquo 症候群卵巢的肿瘤胃的癌症肋膜的流出腹水