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Morphomics via next-generation electron microscopy

Journal of Molecular Cell Biology 2023年第12期15卷 12-27页

作者： Raku Son Kenji Yamazawa Akiko Oguchi Mitsuo Suga masaru tamura Motoko Yanagita Yasuhiro Murakawa Satoshi Kume RIKEN-IFOM Joint Laboratory for Cancer Genomics RIKEN Center for Integrative Medical SciencesYokohama 230-0045Japan Department of Nephrology Graduate School of MedicineKyoto UniversityKyoto 606-8507Japan Advanced Manufacturing Support Team RIKEN Center for Advanced PhotonicsWako 351-0198Japan Multimodal Microstructure Analysis Unit RIKEN–JEOL Collaboration CenterKobe 650-0047Japan Technology and Development Team for Mouse Phenotype Analysis RIKEN BioResource Research CenterTsukuba 305-0074Japan Institute for the Advanced Study of Human Biology(ASHBi) Kyoto UniversityKyoto 606-8501Japan IFOM—The FIRC Institute of Molecular Oncology Milan 20139Italy Laboratory for Pathophysiological and Health Science RIKEN Center for Biosystems Dynamics ResearchKobe 650-0047Japan Center for Health Science Innovation Osaka City UniversityOsaka 530-0011Japan Osaka Electro-Communication University Neyagawa 572-8530Japan

The living body is composed of innumerable fine and complex *** these structures have been studied in the past,a vast amount of information pertaining to them still remains *** attempting to observe these ultra-structures,the use of electron microscopy(EM)has become ***,conventional EM settings are limited to a narrow tissue area,which can bias ***,new trends in EM research have emerged,enabling coverage of far broader,nano-scale fields of view for two-dimensional wide areas and three-dimensional large ***,cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological *** together,these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology,which now arises as a new omics science termed‘morphomics’.

关键词： comprehensive morphological analysis next-generation electron microscopy 3D bioimaging imaging database deep learning

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Sahara’s surface transformation forced an abrupt hydroclimate decline and Neolithic culture transition in northern China

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The Innovation 2024年第1期5卷 70-79页

作者： Yandong Hou Hao Long Sumiko Tsukamoto Zhengyao Lu Jie Chen Daniel EIbarra Toru tamura Qiong Zhang Weiyi Sun Jingran Zhang Lei Gao Manfred Frechen Ji Shen State Key Laboratory of Lake Science and Environment Nanjing Institute of Geography and LimnologyChinese Academy of Sciences(NIGLAS)Nanjing 210008China Leibniz Institute for Applied Geophysics(LIAG) Department of Geochronology30655 HannoverGermany Department of Physical Geography and Ecosystem Science Lund University22100 LundSweden Key Laboratory of Western China’s Environmental Systems(Ministry of Education) College of Earth and Environmental SciencesLanzhou UniversityLanzhou 730000China College of Atmospheric Sciences Lanzhou UniversityLanzhou 730000China Institute at Brown for Environment and Society and Department of Earth Environmentaland Planetary SciencesBrown UniversityProvidenceRI 02912USA Geological Survey of Japan National Institute of Advanced Industrial Science and TechnologyTsukubaIbaraki 305-8567Japan Graduate School of Frontier Sciences University of TokyoKashiwaChiba 277-8561Japan Department of Physical Geography and Bolin Centre for Climate Research Stockholm University10691 StockholmSweden School of Geography Nanjing Normal UniversityJiangsu Centre for Collaborative Innovation in Geographical Information Resource Development and ApplicationKey Laboratory of Virtual Geographic EnvironmentMinistry of Education of ChinaNanjing 210023China School of Geography and Ocean Science Nanjing UniversityNanjing 210023China

The remote forcing from land surface changes in the Sahara is hypothesized to play a pivotal role in modulating the intensity of the East Asian summer monsoon(EASM)through ocean-atmospheric *** modulation has far-reaching consequences,particularly in facilitating societal shifts documented in northern ***,we present a well-dated lake-level record from the Daihai Lake Basin in northern China,providing quantitative assessments of Holocene monsoonal precipitation and the consequent migrations of the northern boundary of the *** reconstruction,informed by a water-and-energy balance model,indicates that annual precipitation reached700 mm during 8–5 ka,followed by a rapid decline to tween 5 and 4 *** shift coherently aligns with a signi550 mm be-ficant300 km northwestward movement of the EASM northern boundary during the Middle Holocene(MH),in contrast to its current *** findings underscore that these changes cannot be entirely attributed to orbital forcing,as corroborated by simulation *** model simulations deployed in our study suggest that the presence of the Green Sahara during the MH significantly strengthened the EASM and led to a northward shift of the monsoon rainfall ***,the Sahara’s reversion to a desert landscape in the late Holocene was accompanied by a corresponding southward retraction of monsoon *** dramatic hydroclimate changes during5–4 ka likely triggered or at least contributed to a shift in Neolithic cultures and societal transformation in northern *** decreasing agricultural productivity,communities transitioned from millet farming to a mixed rainfed agriculture and animal husbandry ***,our findings elucidate not only the variability of the EASM but also the profound implications of a remote forcing,such as surface transformations of the Sahara,on climatic changes and cultural evolution in northern China.

关键词： Holocene monsoon abrupt

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Advances in endoscopic therapy using grasping-type scissors forceps(with video)

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World Journal of Gastrointestinal Surgery 2021年第8期13卷 772-787页

作者： Kazuya Akahoshi Keishi Komori Kazuaki Akahoshi Shinichi tamura Shigeki Osada Yuki Shiratsuchi masaru Kubokawa Endoscopy Center Aso Iizuka HospitalIizuka 820-8505Japan Department of Gastroenterology Aso Iizuka HospitalIizuka 820-8505Japan

Endoscopic submucosal dissection(ESD)is a globally accepted minimally invasive therapy for early-stage gastrointestinal tract *** numerous electrosurgical knives have been developed for ESD,technical difficulties and high complication rates(bleeding and perforation)have limited their use *** grasping-type scissors forceps[clutch cutter(CC)]is the first forceps-type resection device developed with reference to hemostatic *** aim was to allow easy and safe ESD throughout the gastro-intestinal tract,as a biopsy technique,using one *** CC can grasp the target tissue accurately and pull it away from the underlying muscle layer prior to energizing the tissue,for safe and effective incision and hemostasis during *** clinical studies showed that ESD using the CC(ESD-CC)is a safe(perforation rate:0%-3.6%;delayed bleeding rate:0%-4.2%),technically efficient(en-bloc resection rate:88.9%-100%),and single-device method for dissecting early-stage gastrointestinal tract *** ESD-CC technique is simple and easy to learn because it can be completed simply by repeating the grasp,pull,and coagulate and/or incise actions using an electrosurgical *** reported self-completion rate by nonexperts was significantly better with the CC than with conventional knives(61.7%vs 24.5%,respectively;P<0.001).Furthermore,the CC is used for other endoscopic therapies,such as endoscopic polypectomy for large pedunculated polyps,endoscopic myotomy for Zenker’s diverticulum,endoscopic treatment of buried bumper syndrome,and endoscopic necrosectomy for wall-off pancreatic *** initial reports using CC for these therapies have shown favorable *** this review,we describe the structural features of the CC,how to use the instrument,efficacies of ESD-CC,and other unique endoscopic therapies using the CC.

关键词： Grasping-type scissors forceps Clutch cutter Endoscopic submucosal dissection Endoscopic polypectomy Zenker’s diverticulum Buried bumper syndrome

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Increasing spatial coverage in rough terrain and vegetated areas using InSAR optimized pixel selection:application to Tohoku,Japan

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Geo-Spatial Information Science 2022年第2期25卷 295-311页

作者： Tamer ElGharbawi Masayuki tamura Civil and Earth Resources Engineering Department Kyoto UniversityKyotoJapan

One of the major limitations of using Interferometric Synthetic Aperture Radar(InSAR)in time series analysis is the low-phase coherence associated with rough terrain and vegetated areas,which results in limited spatial coverage in such *** scatterers technique was introduced to overcome this limitation using time-series ***,identifying major scatterers within a pixel requires the single-looked pixels oversampling which can be a demanding process especially with large interferometric stacks and vast study ***,using multilooked temporal coherent pixels was proposed to increase processing efficiency and coverage by utilizing distributed targets,but this technique may exclude pixels with reliable phase returns because of their temporal varying neighboring *** this paper,we propose a technique to identify multilooked temporal stable pixels with reliable phase returns independent of their neighboring *** conduct a simulation analysis to relate the spatial coherence of a pixel with its expected temporal correlation in the time series analysis *** found that a liberal temporal correlation threshold of 0.53 in multilooked pixels stack is equivalent to a spatial coherence threshold of 0.2 when using number of looks of 9,which is considered acceptable in temporal coherent pixels,in terms of phase standard *** these findings to study the 2011 Tohoku earthquake in the northeastern part of Japan resulted in increasing the number of usable pixels and spatial coverage index by nearly 50.4%and 36.8%,respectively,compared to the temporal coherent ***,we propose an approach to integrate GPS observations with InSAR time series analysis,which resulted in deformation maps of the megathrust 2011 Tohoku earthquake with mean RMSE of 11.4 mm and a correlation of 98%in comparison to GPS observations.

关键词： 2011 Tohoku earthquake temporal stable pixels coherence phase noise GPS coverage index

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Alterations of tumor suppressor and tumor-related genes in the development and progression of gastric cancer

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World Journal of Gastroenterology 2006年第2期12卷 192-198页

作者： Gen tamura Department of Pathology Yamagata University School of MedicineYamagata 990-9585Japan

The development and progression of gastric cancer involves a number of genetic and epigenetic alterations of tumor suppressor and tumor-related genes. The majority of differentiated carcinomas arise from intestinal metaplastic mucosa and exhibit structurally altered tumor suppressor genes, typified by p53, which is inactivated via the classic two-hit mechanism, i.e. loss of heterozygosity （LOH） and mutation of the remaining allele. LOH at certain chromosomal loci accumulates during tumor progression. Approximately 20% of differentiated carcinomas show evidence of mutator pathway tumorigenesis due to hMLH1 inactivation via hypermethylation of promoter CpG islands, and exhibit high-frequency microsatellite instability. In contrast, undifferentiated carcinomas rarely exhibit structurally altered tumor suppressor genes. For instance, while methylation of E-cadherin is often observed in undifferentiated carcinomas, mutation of this gene is generally associated with the progression from differentiated to undifferentiated carcinomas. Hypermethylation of tumor suppressor and tumor-related genes, including APC, CHFR, DAP- kinase, DCC, E-cadherin, GSTP1, hMLH1, p16, PTEN, RASSF1A, RUNX3, and TSLC1, can be detected in both differentiated and undifferentiated carcinomas at varying frequencies. However, the significance of the hypermethylation varies according to the analyzed genomic region, and hypermethylation of these genes can also be present in non-neoplastic gastric epithelia. Promoter demethylation of specific genes, such as MAGE and synudein y, can occur during the progressive stages of both histological types, and is associated with patient prognosis. Thus, while the molecular pathways of gastric carcinogenesis are dependent on histological background, specific genetic alterations can still be used for risk assessment, diagnosis, and prognosis.

关键词： Gastric cancer p53 E-cadherin hMLH1 Methylation

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Pediatric kidney transplantation during the COVID-19 pandemic

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World Journal of Clinical Cases 2022年第34期10卷 12494-12499页

作者： Hiroshi tamura Department of Pediatrics Kumamoto UniversityKumamoto 860-8556Japan

A waiting list for non-emergency transplant medical care was recommended in the first half of 2020 due to the coronavirus disease 2019(COVID-19)***,the number of kidney transplants temporarily ***,the waiting list for transplant medical care was lifted in the latter half of 2020 with the establishment of a polymerase chain reaction test system and the spread of infection *** basic stance is to recommend vaccination to posttransplant recipients,recipients,and donors who are scheduled to undergo transplantation,and their families,with the start of vaccine therapy in *** mortality rate of patients undergoing kidney transplants who had COVID-19 is slightly higher than healthy persons,and acute kidney injury was reported to lead to graft ***,pediatric cases of severe disease are rare and without *** transplantation medical care will be continuously provided by implementing infection prevention and treatments based on the latest evidence,promoting donated kidney transplantation,and hoping that pediatric patients with renal failure will grow up healthy,both physically and mentally,and become independent members of society,just like healthy children.

关键词： Kidney transplantation COVID-19 pandemic Children

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Response of understory vegetation over 10 years after thinning in an old-growth cedar and cypress plantation overgrazed by sika deer in eastern Japan

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Forest Ecosystems 2017年第2期4卷 93-102页

作者： Atsushi tamura Masanobu Yamane Division of Forest Research and Nature Restoration Planning Kanagawa Prefecture Natural Environment Conservation Center 657 Nanasawa AtsugiKanagawa 243-072 Japan

Background： Forest management strategies such as thinning have long been used to enhance ecosystem functions, especially in *** in plantations with high deer density, however, may not yield a desired increase in understory vegetation because deer graze on germinating plants after ***, we examine the changes in understory vegetation after thinning in plantations that have been overgrazed by sika deer to provide insight into the effects of thinning on ecosystem functions such as soil conservation and biological ***： We conducted our survey in the Tanzawa Mountains of eastern *** surveyed the change in understory vegetation within and outside of three deer exclosures on a single slope with three levels of understory vegetation cover： sparse（1%, exclosure ＂US＂）, moderate（30%, exclosure ＂MM＂）, and dense（80%, exclosure ＂LD＂） over10 years after a 30% thinning of an old-growth cedar and cypress plantation which was overgrazed by sika ***： Understory vegetation cover, biomass and species richness increased within and outside the ＂US＂ and＂MM＂ exclosures after thinning, and biomass was greater within than outside the exclosures at 10 years after *** species dominated both ＂US＂ and ＂MM＂ exclosures before thinning, and trees and shrubs dominated within the exclosures over time after *** contrast, unpalatable, grazing-tolerant, perennial,and annual species increased outside the ＂US＂ and ＂MM＂ *** noticeable changes were observed within and outside the ＂LD＂ exclosure when compared with the ＂US＂ and ＂MM＂ ***： Our results suggest that thinning a stand by 30% based on volume resulted in an increase in understory vegetation cover mainly composed of both unpalatable and grazing-tolerant species in a plantation forest where understory vegetation is sparse or moderate and sika deer density is *** emphasize that establishing deer exclosures or controlling deer is essential to ma

关键词： Biomass Deer exclosure Grazing-tolerant species Understory cover Unpalatable species

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Dynamic robust optimal reorder point with uncertain lead time and changeable demand distribution

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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2010年第12期11卷 938-945页

作者： Masaki tamura Kazuko MORIZAWA Hiroyuki NAGASAWA Department of Electrical and Information Systems Engineering Graduate School of EngineeringOsaka Prefecture University Osaka Prefectural College of Technology

In fixed order quantity systems,uncertainty in lead time is expressed as a set of scenarios with occurrence probabilities,and the mean and variance in demand distribution are supposed to be changeable according to a known pattern.A new concept of "dynamic robust optimal reorder point" is proposed in this paper and its value is calculated as a "robust optimal reorder point function with respect to reorder time".Two approaches were employed in determining the dynamic optimal reorder *** first is a shortage rate satisfaction approach and the second is a backorder cost minimization *** former aims at finding the minimum value of reorder point at each reorder time which satisfies the condition that the cumulative distribution function (CDF) of shortage rate under a given set of scenarios in lead time is greater than or equal to a basic CDF of shortage rate predetermined by a *** the latter approach,the CDF of closeness of reorder point is defined at each reorder time to express how close to the optimal reorder points under the set of scenarios,and the dynamic optimal reorder point is defined according to stochastic *** numerical examples demonstrate the features of these dynamic robust optimal reorder points.

关键词： Reorder point Lead time Robust optimum Uncertainty Scenario

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IMPROVEMENT OF BUBBLE MODEL FOR CAVITATING FLOW SIMULATIONS

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Journal of Hydrodynamics 2009年第1期21卷 41-46页

作者： tamura Y. MATSUMOTO Y. Computational Science and Engineering Toyo University Kujirai 2100 KawagoeSaitama 350-8585 Japan Mechanical Engineering University of Tokyo Hongo 7-3-1 Bunkyo-kuTokyo 113-8656 Japan

In the present research, a bubble dynamics based model for cavitating flow simulations is extended to higher void fraction region for wider range of applications. The present bubble model is based on the so-called Rayleigh-Plesset equation that calculates a temporal bubble radius with the surrounding liquid pressure and is considered to be valid in an area below a certain void fraction. The solution algorithm is modified so that the Rayleigh-Plesset equation is no more solved once the bubble radius （or void fraction） reaches at a certain value till the liquid pressure recovers above the vapor pressure in order to overcome this problem. This procedure is expected to stabilize the numerical calculation. The results of simple two-dimensional flow field are presented compared with the existing bubble model.

关键词： cavitation model Computational Fluid Dynamics (CFD) cavitation flow Rayleigh-Plesset equation

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Taming heterogeneous rhenium catalysis for the production of biomass-derived chemicals

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Chinese Chemical Letters 2020年第5期31卷 1071-1077页

作者： Keiichi Tomishige Yoshinao Nakagawa Masazumi tamura Department of Applied Chemistry School of EngineeringTohoku UniversityMiyagi 980-857Japan

Rhenium is one of important components for heterogeneous catalysts,which has been recently used for the catalytic reactions related to the production of biomass-derived chemicals such as deoxydehydration of vicinal OH groups,C-O hydrogenolysis,and hydrogenation of carboxylic acids,and so *** oxidation state of Re as a catalytic active species is strongly dependent on the catalytic *** control of the oxidation state of Re species on the catalysts is crucial on the catalyst development.

关键词： Rhenium Oxidation state Deoxydehydration Hydrogenolysis Hydrogenation

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