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BEACH-Domain Proteins Act Together in a Cascade to Mediate Vacuolar Protein Trafficking and Disease Resistance in Arabidopsis

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Molecular Plant 2015年第3期8卷 389-398页

作者： Ooi-kock Teh noriyuki hatsugai Kentaro Tamura Kentaro Fuji Ryo Tabata Katsushi Yamaguch Shuji Shingenobu Masashi Yamada Mitsuyasu Hasebe Shinichiro Sawa Tomoo Shimada Ikuko Hara-Nishimura Graduate School of Science Kyoto University Sakyo-ku Kyoto 606-8502 Japan Research Centre for Cooperative Projects Hokkaido University Kita-ku Sapporo 060-8638 Japan Graduate School of Science and Technology Kumamoto University Kumamoto 860-8555 Japan Functional Genomics Facility National Institute for Basic Biology Okazaki 444-8585 Japan Department of Biology and IGSP Center for Systems Biology Duke University Durham NC 27708 USA Division of Evolutionary Biology National Institute for Basic Biology Okazaki 444-8585 Japan School of Life Science The Graduate University for Advanced Studies Okazaki 444-8585 Japan Present address: Department of Plant Biology and Forest Genetics Uppsala BioCenter Swedish University of Agricultural Sciences (SLU) and Linnean Centre ofPlant Biology Uppsala SE-75007 Sweden present address: Microbial and Plant Genomics Institute University of Minnesota St Paul MN 55108 USA Present address: RIKEN Innovation Center RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan

Membrane trafficking to the protein storage vacuole （PSV） is a specialized process in seed plants. However, this trafficking mechanism to PSV is poorly understood. Here, we show that three types of Beige and Chediak-Higashi （BEACH）-domain proteins contribute to both vacuolar protein transport and effector- triggered immunity （ETI）. We screened a green fluorescent seed （GFS） library of Arabidopsis mutants with defects in vesicle trafficking and isolated two allelic mutants gfs3 and gfs12 with a defect in seed pro- tein transport to PSV. The gene responsible for the mutant phenotype was found to encode a putative pro- tein belonging to group D of BEACH-domain proteins, which possess kinase domains. Disruption of other BEACH-encoding loci in the gfs12 mutant showed that BEACH homologs acted in a cascading manner for PSV trafficking. The epistatic genetic interactions observed among BEACH homologs were also found in the ETI responses of the gfs12 and gfs12 bchb-1 mutants, which showed elevated avirulent bacterial growth. The GFS12 kinase domain interacted specifically with the pleckstrin homology domain of BchCl. These results suggest that a cascade of multiple BEACH-domain proteins contributes to vacuolar protein transport and plant defense.

关键词： BEACH-domain protein Arabidopsis thaliana vacuolar protein transport protein storage vacuoles,plant immunity

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Performance Comparison of Vision Transformer- and CNN-Based Image Classification Using Cross Entropy: A Preliminary Application to Lung Cancer Discrimination from CT Images

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Journal of Biomedical Science and Engineering 2024年第9期17卷 157-170页

作者： Eri Matsuyama Haruyuki Watanabe noriyuki Takahashi Faculty of Informatics The University of Fukuchiyama Kyoto Japan School of Radiological Technology Gunma Prefectural College of Health Sciences Gunma Japan School of Health Sciences Fukushima Medical University Fukushima Japan

This study evaluates the performance and reliability of a vision transformer (ViT) compared to convolutional neural networks (CNNs) using the ResNet50 model in classifying lung cancer from CT images into four categories: lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), large cell carcinoma (LULC), and normal. Although CNNs have made significant advancements in medical imaging, their limited capacity to capture long-range dependencies has led to the exploration of ViTs, which leverage self-attention mechanisms for a more comprehensive global understanding of images. The study utilized a dataset of 748 lung CT images to train both models with standardized input sizes, assessing their performance through conventional metrics—accuracy, precision, recall, F1 score, specificity, and AUC—as well as cross entropy, a novel metric for evaluating prediction uncertainty. Both models achieved similar accuracy rates (95%), with ViT demonstrating a slight edge over ResNet50 in precision and F1 scores for specific classes. However, ResNet50 exhibited higher recall for LULC, indicating fewer missed cases. Cross entropy analysis showed that the ViT model had lower average uncertainty, particularly in the LUAD, Normal, and LUSC classes, compared to ResNet50. This finding suggests that ViT predictions are generally more reliable, though ResNet50 performed better for LULC. The study underscores that accuracy alone is insufficient for model comparison, as cross entropy offers deeper insights into the reliability and confidence of model predictions. The results highlight the importance of incorporating cross entropy alongside traditional metrics for a more comprehensive evaluation of deep learning models in medical image classification, providing a nuanced understanding of their performance and reliability. While the ViT outperformed the CNN-based ResNet50 in lung cancer classification based on cross-entropy values, the performance differences were minor and may not hold c

关键词： Lung Cancer Classification Vision Transformers Convolutional Neural Networks Cross Entropy Deep Learning

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Using Cross Entropy as a Performance Metric for Quantifying Uncertainty in DNN Image Classifiers: An Application to Classification of Lung Cancer on CT Images

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Journal of Biomedical Science and Engineering 2024年第1期17卷 1-12页

作者： Eri Matsuyama Masayuki Nishiki noriyuki Takahashi Haruyuki Watanabe Faculty of Informatics University of Fukuchiyama Kyoto Japan Graduate School of Radiological Sciences International University of Health and Welfare Tochigi Japan School of Health Sciences Fukushima Medical University Fukushima Japan School of Radiological Technology Gunma Prefectural College of Health Sciences Gunma Japan

Cross entropy is a measure in machine learning and deep learning that assesses the difference between predicted and actual probability distributions. In this study, we propose cross entropy as a performance evaluation metric for image classifier models and apply it to the CT image classification of lung cancer. A convolutional neural network is employed as the deep neural network (DNN) image classifier, with the residual network (ResNet) 50 chosen as the DNN archi-tecture. The image data used comprise a lung CT image set. Two classification models are built from datasets with varying amounts of data, and lung cancer is categorized into four classes using 10-fold cross-validation. Furthermore, we employ t-distributed stochastic neighbor embedding to visually explain the data distribution after classification. Experimental results demonstrate that cross en-tropy is a highly useful metric for evaluating the reliability of image classifier models. It is noted that for a more comprehensive evaluation of model perfor-mance, combining with other evaluation metrics is considered essential. .

关键词： Cross Entropy Performance Metrics DNN Image Classifiers Lung Cancer Prediction Uncertainty

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Effect of Wearing a Maxillofacial Prosthesis on Masticatory Rhythm Improvement in Mandibulectomy Patients

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Health 2024年第7期16卷 717-729页

作者： Xuewei Han Mihoko Haraguchi Yuka I. Sumita Marwa Ahmed Aboelez noriyuki Wakabayashi Department of Advanced Prosthodontics Graduate School of Medical and Dental Sciences Tokyo Medical and Dental University (TMDU) Tokyo Japan Department of Partial and Complete Denture School of Life Dentistry at Tokyo The Nippon Dental University Tokyo Japan Department of Prosthodontics Faculty of Dentistry Mansoura University Mansoura Egypt

Background: Recording jaw movement rhythms in patients with jaw defects is challenging using conventional tracking devices. However, masticatory rhythm is crucial for masticatory performance and nutritional intake. This study aimed to explore the impact of using a maxillofacial prosthesis to restore masticatory rhythm in mandibulectomy patients with a novel wearable device. Methods: Twelve patients who underwent mandibulectomy and were rehabilitated with maxillofacial prosthesis were recruited. Chewing rate, cycle durations, coefficient of variation of cycle durations (CV), changing times of skin morphology on the back of the ear pinna area (SM), and masticatory performance were measured during gum chewing without and with a denture using a wearable jaw movement rhythm tracking device. A paired t-test and the Pearson correlation coefficient were used for statistical analysis. Results: The chewing rate increased by 8.6 cycles/min with dentures (P P = 0.01). The CV and SM decreased with dentures (P = 0.004 and P = 0.01, respectively). Significant correlations were found between the CV and SM without dentures (P = 0.004). Conclusion: 1. Wearing maxillofacial prostheses can improve masticatory rhythm in patients who undergo mandibulectomy with Eichner B2 occlusal supports. 2. The wearable device is available for measuring masticatory rhythm in patients with jaw defects in clinics. 3. Changing times of the skin morphology on the back of the ear pinna indicate jaw movement stability through a simpler process than the coefficient of variation of cycle durations.

关键词： Masticatory Rhythm Jaw Movement Rhythm Tracking Device Maxillofacial Prosthesis Head and Neck Tumor Mandibulectomy

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Redox active ionic liquid as efficient mediator and solvent for visible light-driven B_(12) catalytic reactions

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Green Energy & Environment 2019年第2期4卷 116-120页

作者： Hisashi Shimakoshi noriyuki Houfuku Li Chen Yoshio Hisaeda Department of Chemistry and Biochemistry Graduate School of Engineering Kyushu University

The redox active ionic liquid, 1-ethyl-4-(methoxycarbonyl)pyridinium bis(trifluoromethanesulfonyl)amide(RIL), was synthesized from its iodide form by an anion exchange reaction of Li(NTf_2) with viscos liquid(η= 122 cP at 25C) and characterized by NMR, IR, and elemental analysis. The compound showed reversible redox couples at -0.65 V and -1.48 V vs. Ag/AgCl and worked as an electron mediator in the B_(12) complex/[Ru(bpy)_3]Cl_2 photosensitizer catalytic system under visible light irradiation. The catalytic efficiency in the RIL was higher than those in DMF, MeOH, and the redox inactive ionic liquid, 1-butyl-3-methyl imidazolium bis(trifluoromethylsulfonyl)amide.

关键词： Ionic liquid Photosensitizer Redox active Visible light Vitamin B12

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Physical Properties of Liquid Terbium Measured by Levitation Techniques

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Journal of Rare Earths 2007年第6期25卷 665-669页

作者： Paul-Francois Paradis Takehiko Ishikawa noriyuki Koike Yuki Watanabe Japan Aerospace Exploration Agency Institute of Space and Astronautical Science ISS Science Project Office 2-1-1 Sengen Tsukuba Ibaraki 305-8505 Japan Chiba Institute of Technology Tsudanuma Narashino Chiba Japan Advanced Engineering Service Co. Ltd. Tsukuba Ibaraki 305-0032 Japan

To understand the nature and behavior of rare earth metals in their liquid phases, accurate values of their physical properties are essential. However, to measure their physical properties, the samples should be maintained in liquid phases for prolonged time, and this raises a formidable challenge. This is mainly explained by their high melting temperatures （e.g., 1629 K for Tb）, high vapor pressure, and the risk of melt contamination with a crucible or support. An electrostatic levitation furnace alleviated these difficulties and allowed the determination of density, surface tension, and viscosity of several metals above their melting temperature. Here, first, the levitation furnace facility and the noncontact diagnostic procedures were briefly discussed, followed by the explanation of their thermophysical property measurements over wide temperature ranges. The density was obtained using an ultraviolet-based imaging technique that allowed excellent illumination, even at elevated temperatures. Over the 1615 to 1880 K temperature span, the density measurements could be expressed as p（T） =7.84 × 10^3 -0.47 （T - Tm）（kg · m^-3） with Tm = 1629 K, yielding a volume expansion coefficient a（T） = 6.0 × 10^-5 （K^-1）. In addition, the surface tension and the viscosity could be determined by inducing a drop oscillation to a molten sample. Using this technique, the surface tension data could be expressed as σ（T） = 8.93 × 10^2 - 0.10 （T - Tm）（mN· m^-1） and those for viscosity as η（T） =0.583 exp [4.1 × 10^4/（RT）] （MPa·s） over the 1690 to 1980 K temperature range

关键词： levitation liquid noncontact terbium rare earths

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Effects of Vertical Angle of Conical Punch on Stretch Flangeability of High Strength Steel

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Acta Metallurgica Sinica(English Letters) 2015年第12期28卷 1503-1509页

作者： Yasuhiro Ito Yoshiaki Nakazawa Yukihisa Kuriyama Katsuyuki Suzuk noriyuki Suzuki Nippon Steel and Sumitomo Metal Corporation The University of Tokyo

To clarify the effects of the vertical angle of a conical punch on stretch flangeability, hole expansion forming tests were conducted. Test results showed that the hole expansion ratio becomes larger as the vertical angle *** also showed that the fracture strain at the fracture location on the hole edge was constant and independent of the vertical angle. This is because the hole expansion ratio was controlled not only by the fracture strain, which is independent of the vertical angle, but also by deformation uniformity along the hole edge. From the result of numerical analyses, it was determined that deformation uniformity depends on the gradient of circumferential stress along the radius direction. When the vertical angle is sharp, the circumferential stress showed a steep decline and the deformation localization was suppressed. Consequently, the hole edge deformed more uniformly and the hole expansion ratio became larger. It is concluded that in order to improve stretch flangeability of high strength steel, it is important to uniformly deform the hole edge by applying a conical punch with a sharp vertical angle.

关键词： Formability Ductile fracture Finite element analysis Hole expansion test

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有机固体废弃物热解气掺氨预混旋流火焰结构研究

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燃烧科学与技术 2024年第3期30卷 239-247页

作者：郭怡君陈达南李兴李军赖诗妮黄宏宇小林敬幸中国科学院广州能源研究所广州510640 中国科学技术大学工程科学学院合肥230027 中国科学技术大学能源科学与技术学院广州510640 江西省碳中和研究中心南昌330096 名古屋大学化学工程系名古屋464-8603

由于有机固废热解产生的热解气热值较低,在一些燃烧器中无法燃烧,故采用旋流和掺混无碳燃料氨气的燃烧方式,以增强热解气燃烧的稳定性并减少碳排放.采用化学发光法对火焰结构进行了实验研究,基于CCD摄像系统,获得了不同当量比和掺氨比... 详细信息

由于有机固废热解产生的热解气热值较低,在一些燃烧器中无法燃烧,故采用旋流和掺混无碳燃料氨气的燃烧方式,以增强热解气燃烧的稳定性并减少碳排放.采用化学发光法对火焰结构进行了实验研究,基于CCD摄像系统,获得了不同当量比和掺氨比下热解气/氨气/空气预混旋流火焰中OH^(*)的化学发光分布.结果表明,不同类型热解气的旋流火焰形态结构差异较大;当量比增加到φ≥1时,OH^(*)辐射强度增强;掺氨使得热解气燃烧极限范围变窄,氨气的添加不仅会抑制OH^(*)自由基的产生,且会对火焰结构产生影响.

关键词：热解气体氨气旋流燃烧预混火焰 OH^(*)化学发光

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Rapidly deforming gastric carcinosarcoma with osteoblastic component:An autopsy case report

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World Journal of Gastroenterology 2012年第30期18卷 4064-4068页

作者： Hiroshi Yoshida noriyuki Tanaka Naobumi Tochigi Yoshio Suzuki Department of Pathology Asahi General HospitalChiba 289-2511Japan

Carcinosarcomas are rare,malignant,biphasic tumors simultaneously comprising carcinoma and sarcoma in a single *** present an extremely rare case of gastric carcinosarcoma with an osteoblastic component that drastically changed its shape within 2 mo.A 59-year-old male patient presented to the emergency outpatient unit with a complaint of black *** endoscopy showed an ulcerated mass in the cardia of the lesser curvature of the *** specimens revealed only *** months later,the ulcerated lesion drastically changed its shape into an exophytic *** gastrectomy was *** the resected specimen,the gastric tumor contained both adenocarcinoma and sarcoma components with lace-like *** patient died 7 mo after the operation,and an autopsy was *** the autopsy,widespread metastases were present in the liver,lung,lymph nodes and *** this report,we describe a case of gastric carcinosarcoma and presume its tumorigenesis based on the autopsy findings.

关键词： Carcinosarcoma Stomach Osteoblastic differentiation Autopsy Tumorigenesis

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Free Energy Change of Micelle Formation for Sodium Dodecyl Sulfate from a Dispersed State in Solution to Complete Micelles along Its Aggregation Pathways Evaluated by Chemical Species Model Combined with Molecular Dynamics Calculations

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物理化学学报 2018年第10期34卷 1163-1170页

作者： YOSHII noriyuki KOMORI Mika KAWADA Shinji TAKABAYASHI Hiroaki FUJIMOTO Kazushi OKAZAKI Susumu Center for Computational Science Graduate School of EngineeringNagoya UniversityNagoya 464-8603Japan Department of Applied Chemistry Nagoya UniversityNagoya 464-8603Japan

Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics(MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run(Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ?G_(i+j)^+, where two aggregates with sizes i and j associate to form the(i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, G_i^+, which was obtained through MD calculations. The calculated ?G_(i+j)^+ was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy ∑_in_i( l,k)G_i^+ and the free energy of mixing ∑_in_i( l,k)k_BTln( n_i( l,k)/n( l,k)), where ni(l, k) is the number of i-mer in the system at the l-th i aggregation path and k-th state, with n(l,k)= ∑_n_i( l,k). All the aggregation pathways were obtained from the initial i state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggre

关键词： Free energy change Aggregation pathway SDS Micelle Molecular dynamics calculation

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