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A COMPREHENSIVE SOFTWARE SUITE FOR THE ANALYSIS OF CDNAS

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Genomics, Proteomics & Bioinformatics 2005年第3期3卷 179-188页

作者： KAZUHARU ARAKAWA HARUO SUZUKI KOSUKE FUJISHIMA KENJI FUJIMOTO SHO UEDA MOTOMU MATSUI masaru tomita INSTITUTE FOR ADVANCED BIOSCIENCES KEIO UNIVERSITY FUJISAWA 252-8520 JAPAN BIOINFORMATICS PROGRAM OF THE GRADUATE SCHOOL OF MEDIA AND GOV- ERNANCE KEIO UNIVERSITY FUJISAWA 252-8520 JAPAN INSTITUTE FOR ADVANCED BIOSCIENCES KEIO UNIVERSITYFUJISAWA 252-8520 JAPAN

We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the proteins they code. Methods implemented include the detection of translation initia- tion and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction. The software package is freely available under the GNU General Public License at http： / /***/ data/cdna/.

关键词： cDNA bioinformatics, software

Serum metabolome profiles characterized by patients with hepatocellular carcinoma associated with hepatitis B and C

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World Journal of Gastroenterology 2016年第27期22卷 6224-6234页

作者： Takafumi Saito Masahiro Sugimoto Kazuo Okumoto Hiroaki Haga Tomohiro Katsumi Kei Mizuno Taketo Nishina Sonoko Sato Kaori Igarashi Hiroko Maki masaru tomita Yoshiyuki Ueno Tomoyoshi Soga Department of Gastroenterology Yamagata University School of Medicine Institute for Advanced Biosciences Keio University

AIM: To clarify the characteristics of metabolite profiles in virus-related hepatocellular carcinoma (HCC) patients using serum metabolome ***: The serum levels of low-molecular-weight metabolites in 68 patients with HCC were quantified using capillary electrophoresis chromatography and mass spectrometry. Thirty and 38 of the patients suffered from hepatitis B virus-related HCC (HCC-B) and hepatitis C virus-related HCC (HCC-C), ***: The main metabolites characteristic of HCC were those associated with glutathione metabolism, notably 13 γ-glutamyl peptides, which are by-products of glutathione induction. Two major profiles, i.e., concentration patterns, of metabolites were identified in HCC patients, and these were classified into two groups: an HCC-B group and an HCC-C group including some of the HCC-B cases. The receiver operating characteristic curve for the multiple logistic regression model discriminating HCC-B from HCC-C incorporating the concentrations of glutamic acid, methionine and γ-glutamyl-glycine-glycine showed a highly significant area under the curve value of 0.94 (95%CI: 0.89-1.0, P < 0.0001).CONCLUSION: The serum levels of γ-glutamyl peptides, as well as their concentration patterns, contribute to the development of potential biomarkers for virus-related HCC. The difference in metabolite profiles between HCC-B and HCC-C may reflect the respective metabolic reactions that underlie the different pathogeneses of these two types of HCC.

关键词： Metabolome Hepatocellular carcinoma γ -glutamyl peptides Glutathione Oxidative stress

Propensity score matching analysis for clinical impact of braided-type versus laser-cut-type covered self-expandable metal stents for endoscopic ultrasound-guided hepaticogastrostomy

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Hepatobiliary & Pancreatic Diseases International 2024年第2期23卷 181-185页

作者： Mitsuki tomita Takeshi Ogura Akitoshi Hakoda Saori Ueno Atsushi Okuda Nobu Nishioka Yoshitaro Yamamoto Hiroki Nishikawa 2nd Department of Internal Medicine Osaka Medical and Pharmaceutical UniversityOsakaJapan Endoscopy Center Osaka Medical and Pharmaceutical UniversityOsakaJapan

Background:To prevent stent migration during endoscopic ultrasound-guided hepaticogastrostomy(EUS-HGS),intra-scope channel release technique is important,but is unfamiliar to non-expert *** self-expandable metal stent(SEMS)is an additional factor to prevent stent ***,no compara-tive studies of laser-cut-type and braided-type during EUS-HGS have been *** aim of this study was to compare the distance between the intrahepatic bile duct and stomach wall after EUS-HGS among laser-cut-type and braided-type ***:To evaluate stent anchoring function,we measured the distance between the hepatic parenchyma and stomach wall before EUS-HGS,one day after EUS-HGS,and 7 days after ***,propensity score matching was performed to create a propensity score for using laser-cut-type group and braided-type ***:A total of 142 patients were enrolled in this *** them,24 patients underwent EUS-HGS using a laser-cut-type SEMS,and 118 patients underwent EUS-HGS using a braided-type ***-HGS using the laser-cut-type SEMS was mainly performed by non-expert endoscopists(n=21);EUS-HGS using braided-type SEMS was mainly performed by expert endoscopists(n=98).The distance after 1 day was significantly shorter in the laser-cut-type group than that in the braided-type group[2.00(1.70-3.75)vs.6.90(3.72-11.70)mm,P<0.001].In addition,this distance remained significantly shorter in the laser-cut-type group after 7 *** these results were similar after propensity score matching analysis,the distance between hepatic parenchyma and stomach after 7 days was increased by 4 mm compared with the distance after 1 day in the braided-type *** the other hand,in the laser-cut-type group,the distance after 1 day and 7 days was almost the ***:EUS-HGS using a laser-cut-type SEMS may be safe to prevent stent migration,even in non-expert hands.

关键词： Endoscopic ultrasound-guided hepaticogastrostomy Endoscopic ultrasound-guided biliary drainage Endoscopic retrograde cholangiopancreatography

Low skeletal muscle mass and high visceral adiposity are associated with recurrence of acute cholecystitis after conservative management:A propensity score-matched cohort study

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Hepatobiliary & Pancreatic Diseases International 2024年第1期23卷 64-70页

作者： Yudai Koya Michihiko Shibata Yuki Maruno Yoshitaka Sakamoto Shinji Oe Koichiro Miyagawa Yuichi Honma masaru Harada Department of Gastroenterology Kyushu Rosai HospitalMoji Medical Center3-1 HigashiminatomachiMoji-kuKitakyushu 801-8502Japan Third Department of Internal Medicine School of MedicineUniversity of Occupational and Environmental HealthKitakyushu 807-8555Japan Department of Surgery Kyushu Rosai Hospital Moji Medical CenterKitakyushu 801-8502Japan

Background:Recurrent acute cholecystitis(RAC)can occur after non-surgical treatment for acute cholecystitis(AC),and can be more severe in comparison to the first episode of *** skeletal muscle mass or adiposity have various effects in several *** aimed to clarify the relationship between RAC and body ***:Patients with AC who were treated at our hospital between January 2011 and March 2022 were *** psoas muscle mass and adipose tissue area at the third lumbar level were measured using computed tomography at the first episode of *** areas were divided by height to obtain the psoas muscle mass index(PMI)and subcutaneous/visceral adipose tissue index(SATI/VATI).According to median VATI,SATI and PMI values by sex,patients were divided into the high and low PMI *** performed propensity score matching to eliminate the baseline differences between the high PMI and low PMI groups and analyzed the cumulative incidence and predictors of ***:The entire cohort was divided into the high PMI(n=81)and low PMI(n=80)*** the propensity score-matched cohort there were 57 patients in each *** Kaplan-Meier analysis,the low PMI group and the high VATI group had a significantly higher cumulative incidence of RAC than their counterparts(log-rank P=0.001 and 0.015,respectively).In a multivariate Cox regression analysis,the hazard ratios of low PMI and low VATI for RAC were 5.250(95%confidence interval 1.083-25.450,P=0.039)and 0.158(95%confidence interval:0.026-0.937,P=0.042),***:Low skeletal muscle mass and high visceral adiposity were independent risk factors for RAC.

关键词： Acute cholecystitis Low skeletal muscle mass Recurrent acute cholecystitis Sarcopenia Visceral adiposity

TiO₂-PES Fibrous Composite Material for Ammonia Removal Using UV-A Photocatalyst

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Journal of Materials Science and Chemical Engineering 2024年第1期12卷 1-19页

作者： Anh Phuong Le Thi masaru Ohshiro Takaomi Kobayashi Department of Science and Technology Innovation Nagaoka University of Technology Nagaoka Japan Kasai Corporation Niigata Japan

This study focused on the development and characterization of TiO2-PES composite fibers with varying TiO2 loading amounts using a phase inversion process. The resulting composite fibers exhibited a sponge-like structure with embedded TiO2 nanoparticles within a polymer matrix. Their photocatalytic performance for ammonia removal from aqueous solutions under UV-A light exposure was thoroughly investigated. The findings revealed that PeTi8 composite fibers displayed superior adsorption capacity compared to other samples. Moreover, the study explored the impact of pH, light intensity, and catalyst dosage on the photocatalytic degradation of ammonia. Adsorption equilibrium isotherms closely followed the Langmuir model, with the results indicating a correlation between qm values of 2.49 mg/g and the porous structure of the adsorbents. The research underscored the efficacy of TiO2 composite fibers in the photocatalytic removal of aqueous under UV-A light. Notably, increasing the distance between the photocatalyst and the light source resulted in de-creased hydroxyl radical concentration, influencing photocatalytic efficiency. These findings contribute to our understanding of TiO2 composite fibers as promising photocatalysts for ammonia removal in water treatment applications.

关键词： Ammonia Removal Photocatalyst TiO2-PES Composite Fiber Fibrous Material

Development and Evaluation of 3D Delivery Animation Software Designed to Improve the Mother’s and Spouse’s Satisfaction with Delivery

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Health 2024年第5期16卷 439-458页

作者： Ayako Sasaki Sachi Chikazawa Nojima Kumiko tomita Takako Hatakeyama Keiko Imoto Yasufumi Imoto Nobutane Faculty of Nursing Osaka Medical and Pharmaceutical University Takatsuki Japan Imoto Ladies Clinic Echizen Japan

Purpose: To clarify the effectiveness of 3-D delivery animation software for the mother’s and husband’s satisfaction with delivery. Subjects and Method: We independently developed a software application used to display the pelvic region and explain the labor process. The study involved a collaboration with hospital staff who recruited 18 primiparous and 18 multiparous mothers who were hospitalized for delivery at Facility A. The midwife explained the process of delivery using the “Delivery Animation Software”. A self-administered, anonymous questionnaire was distributed and analyzed separately for primiparous and multiparous mothers and their husbands. Results: 1) For both primiparous and multiparous couples, both mothers and their husbands gained a significantly higher level of understanding after delivery than during pregnancy. 2) The Self-Evaluation Scale for Experience of Delivery results were as follows: “I did my best for the baby even if it was painful” was selected more often for “birth coping skills”;“reliable medical staff” was selected more often for “physiological birth process”;“the birth progressed as I expected” was selected frequently by primiparous mothers;and “the birth progressed smoothly” was selected often by multiparous mothers. 3) In terms of husbands’ satisfaction with the delivery, “I was satisfied with the delivery”, “I was given an easy-to-understand explanation”, and “They explained the process to me” was selected of primiparous and multiparous fathers. 4) All primiparous and multiparous mothers positively evaluated whether the delivery animation was helpful in understanding the process of delivery. Conclusion: The delivery animation was effective in improving the understanding and satisfaction of both the mothers and their husbands.

关键词： Mother Spouse Satisfaction 3D Delivery Animation Software

glpK和rpoC基因突变对大肠杆菌生长的调节机制

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glpK和rpoC基因突变对大肠杆菌生长的调节机制

Prophylactic Pattern Scanning Laser Retinal Photocoagulation for Diabetic Retinopathy in Spontaneously Diabetic Torii Fatty Rats: Preliminary Experimental Results

第十八届全国波谱学学术年会

作者： Kian-Kai Cheng Baek-Seok Lee Takeshi Masuda Takuro Ito Kazutaka Ikeda Akiyoshi Hirayama Lingli Deng Jiyang Dong Kazuyuki Shimizu Tomoyoshi Soga masaru tomita Bernhard O.Palsson Martin Robert Institute for Advanced Biosciences Keio UniversityTsuruokaYamagata 997-0017Japan Systems Biology Program Graduate School of Media and GovernanceKeio UniversityKanagawa 252-8520Japan Institute of Bioproduct Development & Department of Bioprocess Engineering Universiti Teknologi Malaysia81310 JohorMalaysia PRESTO Japan Science and Technology AgencyKawaguchiSaitama 332-0012Japan Department of Electronic Science Xiamen University Kyushu Institute of Technology IizukaFukuoka820-8502Japan Department of Bioengineering University of CaliforniaSan DiegoLa JollaCA 92093-0412USA

＜正＞自2006年开始,基因组的重新测序有效地鉴定了细菌适于新环境时所引起的基因突变[1]。然而,相关的促生长机制还没有得到很好的诠释。本文联合利用代谢组学、蛋白质组学和脂类组学的方法对适于甘油的进化菌株中的glpK和rpoC两个基...

＜正＞自2006年开始,基因组的重新测序有效地鉴定了细菌适于新环境时所引起的基因突变[1]。然而,相关的促生长机制还没有得到很好的诠释。本文联合利用代谢组学、蛋白质组学和脂类组学的方法对适于甘油的进化菌株中的glpK和rpoC两个基因突变[2,3]的促生长机制进行深入研究,结果表明:进化大肠杆菌细胞株是通过两种不同的代谢方式来实现在甘油培基内更快的增长。首先,rpoC基因27bp的缺失提高了

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Journal of Diabetes Mellitus 2024年第3期14卷 153-165页

作者： Rina Takagi Yoshiaki Tanaka Tetsuya Hasegawa Masami Shinohara Yasushi Kageyama Tomohiko Sasase Machiko Shimmura-tomita Akihiro Kakehashi Toshikatsu Kaburaki Department of Ophthalmology Saitama Medical Center Jichi Medical University Saitama-shi Saitama-ken Japan Tokyo Animal & Diet Department CLEA Japan Inc. Tokyo Japan Biological/Pharmacological Research Laboratories Central Pharmaceutical Research Institute Japan Tobacco Inc. Takatsuki Osaka Japan

Research Background and Purpose: The number of diabetic patients is rapidly increasing, making it crucial to find methods to prevent diabetic retinopathy (DR), a leading cause of blindness. We investigated the effects of prophylactic pattern scanning laser retinal photocoagulation on DR development in Spontaneously Diabetic Torii (SDT) fatty rats as a new prevention approach. Methods: Photocoagulation was applied to the right eyes of 8-week-old Spontaneously Diabetic Torii (SDT) fatty rats, with the left eyes serving as untreated controls. Electroretinography at 9 and 39 weeks of age and pathological examinations, including immunohistochemistry for vascular endothelial growth factor and glial fibrillary acidic protein at 24 and 40 weeks of age, were performed on both eyes. Results: There were no significant differences in amplitude and prolongation of the OP waves between the right and left eyes in SDT fatty rats at 39 weeks of age. Similarly, no significant differences in pathology and immunohistochemistry were observed between the right and left eyes in SDT fatty rats at 24 and 40 weeks of age. Conclusion: Prophylactic pattern scanning retinal laser photocoagulation did not affect the development of diabetic retinopathy in SDT fatty rats.

关键词： Diabetes Pattern Scanning Laser Diabetic Retinopathy Spontaneously Diabetic Torii Fatty Rats Electroretinography

基于一维和三维CFD方法的四级径流式鼓风机扩压器和回流器设计与优化

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风机技术 2024年第3期66卷 47-59页

作者： Vlad Goldenberg Leonid Moroz Ti-shun Zhang Shigeyuki Tomimatsu Masatoshi tomita SoftInWay Inc. USA DMWCorporation Japan

Soft In Way Inc. performed the aerodynamic design of a 4 stages high pressure radial blower with vaneless diffusers and deswirlers for DMW Corporation in 2021. The nominal pressure ratio of the machine is near *** a pressure ratio often characterizes what would typically be called a compressor, especially if the compression work is performed in one stage. For the subject machine of the present study, the compression work is split into 4 *** paper describes the design procedure for this blower, initially focusing in depth on the tradeoffs between work split,rotor diameter, and rotor vane back-sweep angle. The paper then presents a further design and optimization work of different variants of diffuser and deswirler based on aerodynamic performance for this 4 stages radial blower. The number of deswirler blades in the return channel was reduced from 19 to 10 in consideration of manufacturing requirements. To minimize losses in performance due to reduced blade number, several candidates of varied geometry shape deswirler blades were obtained from an automatic design and optimization workflow combining with 3D CFD calculation. All candidates of deswirler were implemented to the entire 4 stages radial blower to analyze machine performance by 3D CFD calculation and the best 10-blade deswirler geometry was determined. 3D CFD analysis shows that 10 blades of deswirler is unable to provide the same pressure rise and efficiency as the original design with 19 blades when all other parts of the design, such as rotor and diffuser are maintained the same. To further improve the blower performance, the similar automatic workflow was applied to study vaned diffuser influence to the blower performance based on the new blower configuration. The number and geometry of best diffuser blades was obtained from the automatic workflow and entire blower performance with vaned diffuser was analyzed and validated by 3D CFD calculation. After finalizing the aerodynamic flow path geome

关键词： Radial Blower Blower Design Blower 1D Analysis Deswirler Diffuser Automatic Optimization 3DCFD Surge Determination