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Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq

American Journal of Molecular Biology 2017年第4期7卷 153-168页

作者： Akira S. Hirao Yoshihiko Onda Rie shimizu-Inatsugi jun Sese Kentaro K. shimizu Tanaka Kenta Sugadaira Research Station Mountain Science Center University of Tsukuba Ueda Japan Sugadaira Montane Research Center University of Tsukuba Ueda Japan Cellulose Production Research Team Biomass Engineering Research Division RIKEN Center for Sustainable Resource Science Yokohama Japan Kihara Institute for Biological Research Yokohama City University Yokohama Japan Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland Artificial Intelligence Research Center National Institute of Advanced Industrial Science and Technology Tokyo Japan

Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations;however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by making individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.

关键词： Arabidopsis kamchatica Allele Frequency Homeolog Individual-Based Genotyping Massive Parallel Sequencing

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Novel dioxygenases for useful amino acid production

Novel dioxygenases for useful amino acid production

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The 12th Japan-China-Korea Joint Symposium on Enzyme Engineering

作者： Makoto Hibi Sakayu shimizu Kenzo Yokozeki jun Ogawa Research Institute for Bioscience Products & Fine Chemicals Ajinomoto Co.Inc.

＜正＞Introductionα-Ketoglutarate-dependent dioxygenases are useful for production of hydroxy amino acids,some of which exert worthwhile physiological activities on the mammals,and also are components of peptide antibiotics and chiral precursors in the chemical synthesis of other *** previously developed practical bioprocess system of（2S,3R,4S）-4-hydroxyisoleucine,which had remarkable anti-diabetic activity,

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Ventricular Fibrillation Caused by Traumatic Coronary Artery Dissection

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Case Reports in Clinical Medicine 2015年第4期4卷 119-123页

作者： jun-ya Ishikawa Naoto Morimura Eri Nagai Kyota Nakamura Makoto shimizu Keiji Uchida Department of Emergency Medicine Yokohama Municipal Citizen’s Hospital Yokohama Japan Advanced Critical Care and Emergency Medical Center Yokohama City University Medical Center Yokohama Japan Department of Anesthesiology Kanagawa Cancer Center Yokohama Japan Department of Cardiology International Goodwill Hospital Yokohama Japan Cardiovascular Center Yokohama City University Medical Center Yokohama Japan

Coronary artery dissection due to blunt chest trauma (traumatic coronary artery dissection [TCAD]) may heal spontaneously, and some surgeons believe that conservative or elective treat-ments are sufficient, provided that there are no progressing ischemic symptoms. However, we report a patient who experienced sudden ventricular fibrillation (VF) during initial medical care for trauma injuries. The 32-year-old woman was riding in a passenger car when an accident occurred, and was subsequently transported to our emergency department. Twelve-lead electrocardiography revealed ST segment elevation in leads II, III, and aVF, although her vital signs remained stable. Therefore, we prioritized assessing the trauma at other sites, and VF suddenly occurred. Coronary angiography was performed with repeated defibrillation and chest compressions, which resulted in recovery of spontaneous circulation. Occlusion was observed in the right coronary artery, which we treated with balloon angioplasty. However, intravascular ultrasonography (IVUS) subsequently revealed coronary artery dissection, a stent was placed, and the patient successfully recovered. Therefore, IVUS may be useful for diagnosing TCAD, and swift intervention is needed if TCAD is detected.

关键词： Coronary Artery Dissection Blunt Chest Trauma Ventricular Fibrillation Acute Myocardial Infarction Intravascular Ultrasonography

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Safety and efficacy of carbon dioxide insufflation during gastric endoscopic submucosal dissection

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World Journal of Gastroenterology 2015年第26期21卷 8195-8202页

作者： jun Takada Hiroshi Araki Fumito Onogi Takayuki Nakanishi Masaya Kubota Takashi Ibuka Masahito shimizu Hisataka Moriwaki Department of Gastroenterology Gifu University Graduate School of Medicine

AIM: To compare the safety and efficacy of carbon dioxide(CO2) and air insufflation during gastric endoscopic submucosal dissection(ESD).METHODS: This study involved 116 patients who underwent gastric ESD between January and December *** eliminating 29 patients who fit the exclusion criteria,87 patients,without known pulmonary dysfunction,were randomized into the CO2 insufflation(n = 36) or air insufflation(n = 51) *** ESD was performed with a CO2 regulation unit(constant rate of 1.4 L/min) used for patients undergoing CO2 *** received diazepam for conscious sedation and pentazocine for *** CO2 tension(Ptc CO2) was recorded 15 min before,during,and after ESD with *** CO2,the correlation between Ptc CO2 and procedure time,and ESD-related complications were compared between the two *** blood gases were analyzed after ESD in the first 30 patients(12 with CO2 and 18 with air insufflation) to assess the correlation between arterial blood CO2 partial pressure(Pa CO2) and Ptc ***: There were no differences in respiratoryfunctions,median sedative doses,or median procedure times between the ***,there was no significant difference in post-ESD blood gas parameters,including Pa CO2,between the CO2 and air groups(44.6 mm Hg vs 45 mm Hg).Both groups demonstrated median p H values of 7.36,and none of the patients exhibited *** significant differences were observed between the CO2 and air groups with respect to baseline Ptc CO2(39 mm Hg vs 40 mm Hg),peak Ptc CO2 during ESD(52 mm Hg vs 51 mm Hg),or median Ptc CO2 after ESD(50 mm Hg vs 50 mm Hg).There was a strong correlation between Pa CO2 and Ptc CO2(r = 0.66; P < 0.001).The incidence of Mallory-Weiss tears was significantly lower with CO2 insufflation than with air insufflation(0% vs 15.6%,P = 0.013).CO2 insufflation did not cause any adverse events,such as CO2 narcosis or gas ***: CO2 insufflation durin

关键词： Carbon dioxide Gastric endoscopic submucosaldissection Insufflation Mallory-Weiss tear Randomizedcontrolled trial

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Distinctive magnetic resonance imaging findings of hepatocellular carcinoma after hepatitis C virus eradication with direct-acting antivirals

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Hepatoma Research 2020年第3期6卷 41-49页

作者： Takao shimizu Kaoru Tsuchiya Masayuki Kurosaki Yutaka Yasui Sakura Kirino Keiya Watakabe Leona Osawa Mao Okada Wan Wang Mayu Higuchi Kenta Takaura Shun Kaneko Nobuharu Tamaki Hiroyuki Nakanishi jun ltakura Yuka Takahashi Tadakazu Hisamatsu Namiki lzumi Department of Gastroenterology and Hepatology Musashino Red Cross HospitalTokyo 180-8610Japan Department of Gastroenterology and Hepatology Kyorin University HospitalTokyo 180-8610Japan

Aim:The aim of the present study was to evaluate the characteristics of the magnetic resonance imaging features of hepatocellular carcinoma(HCC)that developed early after the eradication of hepatitis C virus(HCV)by direct-acting antiviral(DAA)***:This study included 26 patients who achieved sustained viral response with DAA and developed HCC thereafter within one year(DAA-SVR HCC).The radiologic characteristics of these patients were evaluated by contrast-enhanced magnetic resonance imaging,including diffusion-weighted imaging(DWI)and T2-weighted imaging(T2WI).For comparison,80 HCC patients with positive HCV RNA(HCV-positive HCC)were *** 42 patients where tumor biopsy was available,histological grade and radiologic findings were ***:The rates of high intensity on DWI and T2WI were significantly higher in DAA-SVR HCC compared to HCV-positive HCC(DWI:100%vs.67.5%,P<0.001T2WI:92.6%vs.67.5%,P=0.01).HCC with high intensity on DWI or T2WI was more likely to have moderately or poorly differentiated HCC compared to well-differentiated HCC(DWI:69.7%vs.30.3%,P=0.02;T2WI:66.7%vs.27.3%,P=0.03).Conclusion:High intensity on DWI and hyperintensity on T2WI were distinctive features of HCC that developed within one year after the end of DAA treatment.

关键词： Hepatocellular carcinoma direct-acting antivirals sustained viral response contrast enhanced magnetic resonance imaging

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Sr,Nd,Ce,O ISOTOPES AND TRACE ELEMENT GEOCHEMISTRY OF CENOZOIC VOLCANIC ROCKS,KANGSULAKE,YUTIAN COUNTY,XINJIANG

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Chinese Science Bulletin 1990年第17期35卷 1450-1454页

作者：刘丛强解广轰 S.NAKAI H.shimizu A.MASUDA Institute of Geochemistry Academia Sinica Guizhou 550002 PRC Laboratory for REE Microanalysis Department of Chemistry Faculty of Science University of Tokyo Hongo Tokyo 113 Japan

Ⅰ. GEOLOGYSamples studied were collected by LUO Xiang-jun from Kangsulake, Yutiantown. Geology of this area has been given by LIU Jia-qi. Two lava layers can be recognized. The upper layer is 1.1 Ma BP and the lower is 1.4 Ma BP (LUO Xiang-jun, personal communication, 1987). A K-Ar age of 1.24 Ma was obtained by the authors (1988), which is in agreement with the result reported by LIU Jia-qi.

关键词： isotope volcanic rocks mantle Xinjiang.

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Predictors of kidney tubular dysfunction induced by adefovir treatment for chronic hepatitis B

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World Journal of Gastroenterology 2015年第7期21卷 2116-2123页

作者： Motohiro shimizu Norihiro Furusyo Hiroaki Ikezaki Eiichi Ogawa Takeo Hayashi Takeshi Ihara Yuji Harada Kazuhiro Toyoda Masayuki Murata jun Hayashi Department of General Internal Medicine Kyushu University Hospital Kyushu General Internal Medicine Center Haradoi Hospital

AIM:To investigate the predictors of proximal kidney tubular dysfunction(PKTD)induced by adefovir dipivoxil(ADV)treatment for chronic hepatitis ***:Seventy-nine patients(age at the evaluation of PKTD:56.9±10.7 years)with chronic hepatitis B undergoing long-term oral antiviral nucleos(t)ide analogue treatment were consecutively *** was defined by the presence of at least two of the following five abnormalities:phosphate diabetes,nondiabetic glucosuria,metabolic acidosis,β2-microglobulinuria,or renal *** single-nucleotide polymorphisms(SNPs)in the SLC22A6 gene encoding human organic anion transporter 1(h OAT1)and ABCC2 encoding multidrug resistance protein 2(MRP2)were analyzed using the Taq Man Allelic Discrimination Demonstration ***:Nine(30.0%)of the 30 ADV-treated patients were diagnosed with PKTD,while no patients without ADV developed PKTD(P<0.001).Three patients with ADV were diagnosed with symptomatic *** the patients who took ADV,those with PKTD were of higher age at initiation,had significantly longer treatment duration,and had a significantly lower body mass index than those without *** incidence of PKTD dramatically increased after 96 mo from the start of ADV *** contrast,the SNPs were not correlated with *** regression analysis extracted older age at initiation(OR=5.0,95%CI:1.1-23.4;P=0.040)and longer treatment duration(OR=3.2,95%CI:1.2-8.6;P=0.020)as significant factors associated with ***:Our results suggest that the tubular function of the kidney of older patients undergoing longterm ADV treatment should be carefully evaluated.

关键词： Adefovir dipivoxil Proximal kidney tubular dysfunc

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Correlation of prefrontal activity measured by near-infrared spectroscopy (NIRS) with mood, BDNF genotype and serum BDNF level in healthy individuals

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Open Journal of Psychiatry 2012年第3期2卷 194-203页

作者： Daisuke Matsuzawa Kotaro Takeda Hiroyuki Ohtsuka jun Takasugi Takashi Watanabe junko Maeda Saeka Nagakubo Chihiro Sutoh Ichiro Shimoyama Ken Nakazawa Eiji shimizu Clinical Research Center National Hospital Organization Murayama Medical Center Tokyo Japan Department of Cognitive Behavior Physiology Graduate School of Medicine Chiba University Chiba Japan Section for Human Neurophysiology Frontier Medical Engineering Chiba University Chiba Japan

Depression has been known to reduce the prefrontal activity associated with the execution of certain cognitive tasks, although whether a temporarily depressed or anxious mood in healthy individuals affects the prefrontal blood oxygen level during cognitive tasks is unknown. Combining the measurement of prefrontal activity with near-infrared spectroscopy (NIRS) and the two cognitive tasks, namely the letter version of the verbal fluency test (VFT-l) and the Stroop test, we measured the effect of a depressed or anxious mood and gender on the changes in the prefrontal oxygenated hemoglobin (Oxy-Hb) levels during those cognitive tests in healthy individuals. Depressed mood or anxious mood was assessed by the Hospital Anxiety and Depression Scale (HADS). Thereby we aimed to explore the possibility of NIRS measurement for detecting the early subclinical manifestation of major depression. Moreover, we examined the possible relationships between prefrontal activation and the functional Val66Met polymorphisms of the brain derived neurotropic factor (BDNF) gene and serum BDNF level. As a result, the increased prefrontal Oxy-Hb levels during cognitive tasks were significantly correlated with the severity of depressed mood in males. The course of the prefrontal Oxy-Hb increase was different depending on the cognitive tasks, i.e., the VFT-l or the Stroop test, in both genders. Correlations of BDNF genotype and serum BDNF level with the prefrontal Oxy-Hb levels during those cognitive tasks were negative. Our results suggest that the early subclinical manifestation of depressed mood in males might be detected by the NIRS measurement, which is not correlated with the individual properties of BDNF.

关键词： Near-Infrared Spectroscopy (NIRS) Depression Anxiety Brain Derived Neurotropic Factor (BDNF)

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Effect of the Early Introduction of Mild Mobilization Performed by Nurses on the Recovery of Patients in the Intensive Care Unit

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Open Journal of Nursing 2016年第12期6卷 969-976页

作者： Yuta Mitobe Yu Koyama Hagiko Aoki Utako shimizu Yoshiyuki Muramatsu Chikayo Koyama Sayuri Sakai Yuka Iwasa jun Kikunaga Megumi Taguchi Masakazu Nitta Hiroshi Endoh Masaki Kitajima Shinichiro Morishita Niigata University of Health and Welfare Niigata Japan Department of Nursing Niigata University Graduate School of Health Sciences Niigata Japan Division of Emergency Critical Care Medicine Niigata University Graduate School of Medical Niigata Japan Institute for Human Movement and Medical Sciences Niigata University of Health and Welfare Niigata Japan

Rationale: Recent studies have reported the effectiveness of the early introduction of rehabilitation for preventing muscle weakness in patients in the intensive care unit (ICU). The early introduction of full-scale rehabilitation by a physical therapist is difficult in some cases because of disease severity and/or patient conditions. However, mild mobilization by a nurse (MMN), as a part of standard care performed, may have a positive effect on patient recovery. We examined the effect of the early introduction of MMN on the recovery of patients in the ICU. Methods: We retrospectively examined patients admitted to Niigata University Hospital’s ICU during between April 2014 and March 2015 who were receiving mechanical ventilation for 7 days or more. Patients were divided into two groups according to the date of initiation of MMN: group L comprised patients for whom MMN was started after 72 hours and group E comprised patients for whom MMN was started within 72 hours after ICU admission. The data were analyzed using the Fisher test, Mann-Whitney U test, and Wilcoxon test. Statistical significance was defined as P Results: Sixty-three patients were included: 42 patients in group L and 21 in group E. There was no significant difference between the two groups in patients’ background, including the type of illness, steroid use, presence of sepsis or diabetes, and sequential organ failure assessment (SOFA) score on ICU admission;however, the SOFA score at ICU discharge was significantly decreased in group E compared to that in group L (6.21 versus 4.30;P = 0.034). Conclusion: Our results indicate that MMN may reduce disease severity if started within 72 hours after ICU admission.

关键词： Intensive Care Unit (ICU) Nurse Mobilization Sequential Organ Failure Assessment (SOFA) Score

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日本山地森林小流域悬移质泥沙研究

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北京林业大学学报 2005年第6期27卷 14-19页

作者：张建军清水晃壁谷■记延廣竜彦水土保持与荒漠化防治教育部重点实验室北京林业大学水土保持学院日本森林综合研究所

以日本山地源头森林小流域为研究对象,利用泥沙自动取样器和自计水位计,研究了悬移质泥沙的输出过程及其与洪水过程间的关系.研究结果表明,该森林流域的泥沙来源主要是林道、沟道、沟道两边裸露地;河川径流中悬移质泥沙浓度与总泥沙浓... 详细信息

以日本山地源头森林小流域为研究对象,利用泥沙自动取样器和自计水位计,研究了悬移质泥沙的输出过程及其与洪水过程间的关系.研究结果表明,该森林流域的泥沙来源主要是林道、沟道、沟道两边裸露地;河川径流中悬移质泥沙浓度与总泥沙浓度间有很好的相关性;降雨时悬移质泥沙浓度随流量过程的变化呈现出顺时针变化的套索;悬移质泥沙的输出过程属于波浪式变化;悬移质泥沙浓度最大值与洪峰流量几乎同时出现,属同步型;悬移质输沙量主要取决于10 min最大雨量;场降雨量对悬移质输沙量的贡献较大;单场大暴雨造成的悬移质输沙量占全年输沙量的5%左右;悬移质年输沙量的30%是由为数不多的几场降雨造成的.

关键词：悬移质输沙量洪水过程森林流域

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