20 results on '"FUYUKI ISHIKAWA"'
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2. Author Correction: The interferon stimulated gene-encoded protein HELZ2 inhibits human LINE-1 retrotransposition and LINE-1 RNA-mediated type I interferon induction
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Ahmad Luqman-Fatah, Yuzo Watanabe, Kazuko Uno, Fuyuki Ishikawa, John V. Moran, and Tomoichiro Miyoshi
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Science - Published
- 2023
- Full Text
- View/download PDF
3. Hippocampal TERT Regulates Spatial Memory Formation through Modulation of Neural Development
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Qi-Gang Zhou, Meng-Ying Liu, Han-Woong Lee, Fuyuki Ishikawa, Sushil Devkota, Xin-Ru Shen, Xin Jin, Hai-Yin Wu, Zhigang Liu, Xiao Liu, Xun Jin, Hai-Hui Zhou, Eun Jeoung Ro, Jing Zhang, Yu Zhang, Yu-Hui Lin, Hoonkyo Suh, and Dong-Ya Zhu
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Medicine (General) ,R5-920 ,Biology (General) ,QH301-705.5 - Abstract
Summary: The molecular mechanism of memory formation remains a mystery. Here, we show that TERT, the catalytic subunit of telomerase, gene knockout (Tert−/−) causes extremely poor ability in spatial memory formation. Knockdown of TERT in the dentate gyrus of adult hippocampus impairs spatial memory processes, while overexpression facilitates it. We find that TERT plays a critical role in neural development including dendritic development and neuritogenesis of hippocampal newborn neurons. A monosynaptic pseudotyped rabies virus retrograde tracing method shows that TERT is required for neural circuit integration of hippocampal newborn neurons. Interestingly, TERT regulated neural development and spatial memory formation in a reverse transcription activity-independent manner. Using X-ray irradiation, we find that hippocampal newborn neurons mediate the modulation of spatial memory processes by TERT. These observations reveal an important function of TERT through a non-canonical pathway and encourage the development of a TERT-based strategy to treat neurological disease-associated memory impairment. : In this article, Qi-Gang Zhou and colleagues show that spatial memory formation, neural development including dendritic development and neuritogenesis, and neural circuit integration are impaired in Tert gene knockout mice. Hippocampal TERT accounts for these phenotypes in a reverse transcription activity-independent manner. Keywords: telomerase, neural progenitor cells, hippocampus, neural development, circuit integration
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- 2017
- Full Text
- View/download PDF
4. Telomere-binding proteins Taz1 and Rap1 regulate DSB repair and suppress gross chromosomal rearrangements in fission yeast.
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Hiroyuki Irie, Io Yamamoto, Yusuke Tarumoto, Sanki Tashiro, Kurt W Runge, and Fuyuki Ishikawa
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Genetics ,QH426-470 - Abstract
Genomic rearrangements (gross chromosomal rearrangements, GCRs) threatens genome integrity and cause cell death or tumor formation. At the terminus of linear chromosomes, a telomere-binding protein complex, called shelterin, ensures chromosome stability by preventing chromosome end-to-end fusions and regulating telomere length homeostasis. As such, shelterin-mediated telomere functions play a pivotal role in suppressing GCR formation. However, it remains unclear whether the shelterin proteins play any direct role in inhibiting GCR at non-telomeric regions. Here, we have established a GCR assay for the first time in fission yeast and measured GCR rates in various mutants. We found that fission yeast cells lacking shelterin components Taz1 or Rap1 (mammalian TRF1/2 or RAP1 homologues, respectively) showed higher GCR rates compared to wild-type, accumulating large chromosome deletions. Genetic dissection of Rap1 revealed that Rap1 contributes to inhibiting GCRs via two independent pathways. The N-terminal BRCT-domain promotes faithful DSB repair, as determined by I-SceI-mediated DSB-induction experiments; moreover, association with Poz1 mediated by the central Poz1-binding domain regulates telomerase accessibility to DSBs, leading to suppression of de novo telomere additions. Our data highlight unappreciated functions of the shelterin components Taz1 and Rap1 in maintaining genome stability, specifically by preventing non-telomeric GCRs.
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- 2019
- Full Text
- View/download PDF
5. Activities of National Institute of Informatics in Japan.
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MASARU KITSUREGAWA, SHIGEO URUSHIDANI, KAZUTSUNA YAMAJI, HIROKI TAKAKURA, ICHIRO HASUO, IMARI SATO, FUYUKI ISHIKAWA, ISAO ECHIZEN, and KENSAKU MORI
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INTERNET security ,ARTIFICIAL intelligence ,INFORMATION networks ,TELECOMMUNICATION systems ,COMPUTER vision ,DATA management ,ALGORITHMS - Abstract
This article discusses the recent areas of focus at the National Institute of Informatics (NII) in Japan. First, a look at its academic services including SINET6, a backbone network service across Japan and its data platform service, the NII Research Data Cloud. The article also details NII research in computer science with projects in innovative computer vision and engineerable artificial intelligence, as well as applied research projects including a COVID-19 pneumonia diagnosis tool.
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- 2023
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6. Enablers for Smart Cities
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Amal El Fallah Seghrouchni, Fuyuki Ishikawa, Laurent Hérault, Hideyuki Tokuda, Amal El Fallah Seghrouchni, Fuyuki Ishikawa, Laurent Hérault, Hideyuki Tokuda and Amal El Fallah Seghrouchni, Fuyuki Ishikawa, Laurent Hérault, Hideyuki Tokuda, Amal El Fallah Seghrouchni, Fuyuki Ishikawa, Laurent Hérault, Hideyuki Tokuda
- Published
- 2016
7. Fission yeast Stn1 maintains stability of repetitive DNA at subtelomere and ribosomal DNA regions
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Hidenori Nakaoka, Masahiro Takikawa, Junko Kanoh, Sanki Tashiro, Tomoichiro Miyoshi, Io Yamamoto, and Fuyuki Ishikawa
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AcademicSubjects/SCI00010 ,RAD52 ,Telomere-Binding Proteins ,Biology ,DNA, Ribosomal ,chemistry.chemical_compound ,Schizosaccharomyces ,Genetics ,Repeated sequence ,DNA, Fungal ,Ribosomal DNA ,Repetitive Sequences, Nucleic Acid ,Telomere-binding protein ,Recombination, Genetic ,Microbial Viability ,Recombinational DNA Repair ,Telomere ,Subtelomere ,DNA Replication Fork ,Genome integrity, repair and replication ,Cell biology ,DNA-Binding Proteins ,chemistry ,Mutation ,Schizosaccharomyces pombe Proteins ,DNA ,Transcription Factors - Abstract
Telomere binding protein Stn1 forms the CST (Cdc13/CTC1-STN1-TEN1) complex in budding yeast and mammals. Likewise, fission yeast Stn1 and Ten1 form a complex indispensable for telomere protection. We have previously reported that stn1-1, a high-temperature sensitive mutant, rapidly loses telomere DNA at the restrictive temperature due to frequent failure of replication fork progression at telomeres and subtelomeres, both containing repetitive sequences. It is unclear, however, whether Stn1 is required for maintaining other repetitive DNAs such as ribosomal DNA. In this study, we have demonstrated that stn1-1 cells, even when grown at the permissive temperature, exhibited dynamic rearrangements in the telomere-proximal regions of subtelomere and ribosomal DNA repeats. Furthermore, Rad52 and γH2A accumulation was observed at ribosomal DNA repeats in the stn1-1 mutant. The phenotypes exhibited by the stn1-1 allele were largely suppressed in the absence of Reb1, a replication fork barrier-forming protein, suggesting that Stn1 is involved in the maintenance of the arrested replication forks. Collectively, we propose that Stn1 maintains the stability of repetitive DNAs at subtelomeres and rDNA regions.
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- 2021
8. Goal-Aware RSS for Complex Scenarios via Program Logic
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Ichiro Hasuo, Clovis Eberhart, James Haydon, Jérémy Dubut, Rose Bohrer, Tsutomu Kobayashi, Sasinee Pruekprasert, Xiao-Yi Zhang, Erik André Pallas, Akihisa Yamada, Kohei Suenaga, Fuyuki Ishikawa, Kenji Kamijo, Yoshiyuki Shinya, and Takamasa Suetomi
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FOS: Computer and information sciences ,InformationSystems_GENERAL ,Computer Science - Robotics ,Computer Science - Logic in Computer Science ,Control and Optimization ,Artificial Intelligence ,Automotive Engineering ,I.2.9 ,F.4.1 ,Robotics (cs.RO) ,Logic in Computer Science (cs.LO) - Abstract
We introduce a goal-aware extension of responsibility-sensitive safety (RSS), a recent methodology for rule-based safety guarantee for automated driving systems (ADS). Making RSS rules guarantee goal achievement -- in addition to collision avoidance as in the original RSS -- requires complex planning over long sequences of manoeuvres. To deal with the complexity, we introduce a compositional reasoning framework based on program logic, in which one can systematically develop RSS rules for smaller subscenarios and combine them to obtain RSS rules for bigger scenarios. As the basis of the framework, we introduce a program logic dFHL that accommodates continuous dynamics and safety conditions. Our framework presents a dFHL-based workflow for deriving goal-aware RSS rules; we discuss its software support, too. We conducted experimental evaluation using RSS rules in a safety architecture. Its results show that goal-aware RSS is indeed effective in realising both collision avoidance and goal achievement., 33 pages, 18 figures, 1 table. Accepted for publication in IEEE Transactions on Intelligent Vehicles
- Published
- 2022
9. Targeting Patterns of Driving Characteristics in Testing Autonomous Driving Systems
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Fuyuki Ishikawa, Paolo Arcaini, and Xiaoyi Zhang
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Correctness ,Computer science ,search-based testing ,autonomous driving systems ,Measure (physics) ,020207 software engineering ,Mobile robot ,02 engineering and technology ,Planner ,Acceleration ,driving characteristics ,Path (graph theory) ,0202 electrical engineering, electronic engineering, information engineering ,Test suite ,020201 artificial intelligence & image processing ,Motion planning ,path planner ,computer ,Simulation ,computer.programming_language - Abstract
A common approach in testing automated and autonomous driving systems (ADS) consists in running the ADS in a simulator where driving and environmental conditions are specified in terms of scenarios. An important aspect in ADS testing is to cover different driving situations in which the autonomous car must perform different types of maneuvers. In this paper, we consider the path planner of our industry partner; the path planner is responsible for deciding the path that must be followed by the autonomous car. A path is characterized by the driving characteristics (as forward acceleration, lateral acceleration, curvature, and so on) that are needed, at each time point, to implement it. For different driving characteristics, a good test suite should contain a scenario for which the path planner chooses a path that requires the application of the selected driving characteristics for a non-negligible period of time: this means that the characteristics are relevant in that path. With such a test suite, engineers can observe the different types of decision taken by the path planner, and so possibly better assess its correctness. In the paper, we introduce the notion of patterns of driving characteristics, to characterize their interaction (i.e., simultaneous or not) and measure their duration. Exploiting this definition, we propose two search-based approaches (for single and pairs of driving characteristics) to find scenarios in which such patterns occur and their duration is maximized. Experimental results show that the approaches are effective in finding scenarios for which the path planner generates paths where the different driving characteristics occur in terms of the specified pattern.
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- 2021
- Full Text
- View/download PDF
10. Editorial to the theme section on model-based engineering of smart systems
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Fuyuki Ishikawa, Peter Gorm Larsen, and John Fitzgerald
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Smart system ,Architectural engineering ,Computer science ,Modeling and Simulation ,Section (typography) ,Model based engineering ,Theme (computing) ,Software - Published
- 2020
11. Time-Series Analysis of Tumorigenesis in a Murine Skin Carcinogenesis Model
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Yoshimasa Aoto, Yuichi Wakabayashi, Fuyuki Ishikawa, Yasubumi Sakakibara, Tsuyoshi Hachiya, Sumitaka Hase, and Kazuhiro Okumura
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0301 basic medicine ,Skin Neoplasms ,Time Factors ,Carcinogenesis ,lcsh:Medicine ,Biology ,medicine.disease_cause ,Article ,Lesion ,03 medical and health sciences ,Mice ,medicine ,Carcinoma ,Animals ,Longitudinal Studies ,Stage (cooking) ,lcsh:Science ,Mutation ,Multidisciplinary ,lcsh:R ,Cancer ,Genomics ,Sequence Analysis, DNA ,medicine.disease ,Disease Models, Animal ,030104 developmental biology ,Tumor progression ,Cancer research ,Carcinoma, Squamous Cell ,Papilloma ,lcsh:Q ,medicine.symptom - Abstract
Recent years have witnessed substantial progress in understanding tumor heterogeneity and the process of tumor progression; however, the entire process of the transition of tumors from a benign to metastatic state remains poorly understood. In the present study, we performed a prospective cancer genome-sequencing analysis by employing an experimental carcinogenesis mouse model of squamous cell carcinoma to systematically understand the evolutionary process of tumors. We surgically collected a part of a lesion of each tumor and followed the progression of these tumors in vivo over time. Comparative time-series analysis of the genomes of tumors with different fates, i.e., those that eventually metastasized and regressed, suggested that these tumors acquired and inherited different mutations. These findings suggest that despite the occurrence of an intra-tumor selection event for malignant alteration during the transformation from early- to late-stage papilloma, the fate determination of tumors might be determined at an even earlier stage.
- Published
- 2018
12. Fission yeast Stn1 is crucial for semi-conservative replication at telomeres and subtelomeres
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Fuyuki Ishikawa, Masahiro Takikawa, and Yusuke Tarumoto
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0301 basic medicine ,DNA Replication ,Semiconservative replication ,Genes, Fungal ,Telomere-Binding Proteins ,Biology ,Genome Integrity, Repair and Replication ,Cyclin B ,medicine.disease_cause ,03 medical and health sciences ,chemistry.chemical_compound ,Schizosaccharomyces ,Genetics ,medicine ,DNA, Fungal ,Gene ,Telomere Shortening ,Mutation ,DNA replication ,Fungal genetics ,Temperature ,Telomere ,Subtelomere ,Repressor Proteins ,030104 developmental biology ,chemistry ,Mutagenesis ,Schizosaccharomyces pombe Proteins ,DNA ,DNA Damage - Abstract
The CST complex is a phylogenetically conserved protein complex consisting of CTC1/Cdc13, Stn1 and Ten1 that protects telomeres on linear chromosomes. Deletion of the fission yeast homologs stn1 and ten1 results in complete telomere loss; however, the precise function of Stn1 is still largely unknown. Here, we have isolated a high-temperature sensitive stn1 allele (termed stn1-1). stn1-1 cells abruptly lost telomeric sequence almost completely at the restrictive temperature. The loss of chromosomal DNA happened without gradual telomere shortening, and extended to 30 kb from the ends of chromosomes. We found transient and modest single-stranded G-strand exposure, but did not find any evidence of checkpoint activation in stn1-1 at the restrictive temperature. When we probed neutral-neutral 2D gels for subtelomere regions, we found no Y-arc-shaped replication intermediates in cycling cells. We conclude that the loss of telomere and subtelomere DNAs in stn1-1 cells at the restrictive temperature is caused by very frequent replication fork collapses specifically in subtelomere regions. Furthermore, we identified two independent suppressor mutants of the high-temperature sensitivity of stn1-1: a multi-copy form of pmt3 and a deletion of rif1. Collectively, we propose that fission yeast Stn1 primarily safeguards the semi-conservative DNA replication at telomeres and subtelomeres.
- Published
- 2016
13. Telomere-binding proteins Taz1 and Rap1 regulate DSB repair and suppress gross chromosomal rearrangements in fission yeast
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Yusuke Tarumoto, Kurt W. Runge, Sanki Tashiro, Hiroyuki Irie, Io Yamamoto, and Fuyuki Ishikawa
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Genome instability ,Cancer Research ,DNA Repair ,Yeast and Fungal Models ,QH426-470 ,Biochemistry ,Shelterin Complex ,Schizosaccharomyces Pombe ,0302 clinical medicine ,DNA Breaks, Double-Stranded ,Cell Cycle and Cell Division ,Genetics (clinical) ,Telomere-binding protein ,Gene Rearrangement ,0303 health sciences ,Chromosome Biology ,Chromosomal Deletions ,Eukaryota ,Cell biology ,Chromosomal Aberrations ,Nucleic acids ,Telomeres ,Experimental Organism Systems ,Cell Processes ,Saccharomyces Cerevisiae ,Research Article ,Chromosome Structure and Function ,DNA repair ,Telomere-Binding Proteins ,Biology ,Research and Analysis Methods ,Chromosomes ,Non-Homologous End Joining ,Genomic Instability ,03 medical and health sciences ,Saccharomyces ,Telomere Homeostasis ,Model Organisms ,Schizosaccharomyces ,Genetics ,Point Mutation ,Molecular Biology Techniques ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Organisms ,Fungi ,Biology and Life Sciences ,Gene rearrangement ,Cell Biology ,DNA ,Shelterin ,biology.organism_classification ,Yeast ,Telomere ,enzymes and coenzymes (carbohydrates) ,Schizosaccharomyces pombe ,Mutation ,Animal Studies ,Schizosaccharomyces pombe Proteins ,030217 neurology & neurosurgery ,Cloning - Abstract
Genomic rearrangements (gross chromosomal rearrangements, GCRs) threatens genome integrity and cause cell death or tumor formation. At the terminus of linear chromosomes, a telomere-binding protein complex, called shelterin, ensures chromosome stability by preventing chromosome end-to-end fusions and regulating telomere length homeostasis. As such, shelterin-mediated telomere functions play a pivotal role in suppressing GCR formation. However, it remains unclear whether the shelterin proteins play any direct role in inhibiting GCR at non-telomeric regions. Here, we have established a GCR assay for the first time in fission yeast and measured GCR rates in various mutants. We found that fission yeast cells lacking shelterin components Taz1 or Rap1 (mammalian TRF1/2 or RAP1 homologues, respectively) showed higher GCR rates compared to wild-type, accumulating large chromosome deletions. Genetic dissection of Rap1 revealed that Rap1 contributes to inhibiting GCRs via two independent pathways. The N-terminal BRCT-domain promotes faithful DSB repair, as determined by I-SceI-mediated DSB-induction experiments; moreover, association with Poz1 mediated by the central Poz1-binding domain regulates telomerase accessibility to DSBs, leading to suppression of de novo telomere additions. Our data highlight unappreciated functions of the shelterin components Taz1 and Rap1 in maintaining genome stability, specifically by preventing non-telomeric GCRs., Author summary Tips of chromosomes, telomeres, are bound and protected by a telomere-binding protein complex called shelterin. Most previous studies focused on shelterin’s telomere-specific role, and its general role in genome maintenance has not been explored extensively. In this study, we first set up an assay measuring the spontaneous formation rate per cell division of gross chromosomal rearrangements (GCRs) in fission yeast. We found that the rate of GCRs is elevated in mutants defective for shelterin components Taz1 or Rap1. Detailed genetic experiments revealed unexpectedly that Taz1 and Rap1 have a novel role in repairing DNA double-strand breaks (DSBs) and suppressing GCRs at non-telomeric regions. Given that shelterin components are conserved between fission yeast and humans, future studies are warranted to test whether shelterin dysfunction leads to genome-wide GCRs, which are frequently observed in cancers.
- Published
- 2019
14. Adapting SQuaRE for Quality Assessment of Artificial Intelligence Systems
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Fuyuki Ishikawa and Hiroshi Kuwajima
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FOS: Computer and information sciences ,Computer Science - Machine Learning ,Computer science ,Quality assessment ,business.industry ,media_common.quotation_subject ,02 engineering and technology ,Software quality ,Machine Learning (cs.LG) ,Software Engineering (cs.SE) ,Computer Science - Computers and Society ,Computer Science - Software Engineering ,Trustworthiness ,Software ,020204 information systems ,Computers and Society (cs.CY) ,Square (cipher) ,0202 electrical engineering, electronic engineering, information engineering ,020201 artificial intelligence & image processing ,Quality (business) ,Applications of artificial intelligence ,Software system ,Software engineering ,business ,media_common - Abstract
More and more software practitioners are tackling towards industrial applications of artificial intelligence (AI) systems, especially those based on machine learning (ML). However, many of existing principles and approaches to traditional systems do not work effectively for the system behavior obtained by training not by logical design. In addition, unique kinds of requirements are emerging such as fairness and explainability. To provide clear guidance to understand and tackle these difficulties, we present an analysis on what quality concepts we should evaluate for AI systems. We base our discussion on ISO/IEC 25000 series, known as SQuaRE, and identify how it should be adapted for the unique nature of ML and $\textit{Ethics guidelines for trustworthy AI}$ from European Commission. We thus provide holistic insights for quality of AI systems by incorporating the ML nature and AI ethics to the traditional software quality concepts.
- Published
- 2019
15. Modelling and analysing resilient cyber-physical systems
- Author
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Hausi A. Müller, Gabriel A. Moreno, Zhi Jin, Michele Loreti, Schahram Dustdar, Danny Weyns, Zhenjiang Hu, Fuyuki Ishikawa, Radu Calinescu, Laura Nenzi, Liliana Pasquale, Marin Litoiu, Shinichi Honiden, Jeff Kramer, Bashar Nuseibeh, Timo Kehrer, Heinz W. Schmidt, Christos Tsigkanos, Carlo Ghezzi, Wolfgang Reisig, Kenji Tei, Amel Bennaceur, Haiyan Zhao, The Open University [Milton Keynes] (OU), Politecnico di Milano [Milan] (POLIMI), National Institute of Informatics (NII), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of York [York, UK], Vienna University of Technology (TU Wien), Information Processsing Laboratory (IPL), The University of Tokyo (UTokyo), Software Engineering Institute, Peking University [Beijing], Department of Computer Science [York] (CS-YORK), Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Department of Computer Science [Victoria], University of Victoria [Canada] (UVIC), Università degli Studi di Firenze = University of Florence (UniFI), Photonique THz - IEMN (PHOTONIQUE THz - IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Marin Litoiu, Siobhán Clarke, Kenji Tei, Bennaceur, A., Ghezzi, C., Tei, K., Kehrer, T., Weyns, D., Calinescu, R., Dustdar, S., Hu, Z., Honiden, S., Ishikawa, F., Jin, Z., Kramer, J., Litoiu, M., Loreti, M., Moreno, G., Muller, H., Nenzi, L., Nuseibeh, B., Pasquale, L., Reisig, W., Schmidt, H., Tsigkanos, C., Zhao, H., and SFI
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computation ,Difficult problem ,Computer science ,Adaptive methods for CPS ,02 engineering and technology ,[INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE] ,medical devices ,[INFO.INFO-IU]Computer Science [cs]/Ubiquitous Computing ,Cyber Physical Systems ,Exemplars of CPS ,Theoretical foundations of CPS ,0202 electrical engineering, electronic engineering, information engineering ,Software system ,Dynamism ,Building automation ,Focus (computing) ,business.industry ,Cyber-physical system ,020207 software engineering ,Cyber Physical System ,Data science ,13. Climate action ,smart buildings ,Key (cryptography) ,020201 artificial intelligence & image processing ,Robot operating system ,business - Abstract
International audience; From smart buildings to medical devices to smart nations, software systems increasingly integrate computation, networking, and interaction with the physical environment. These systems are known as Cyber-Physical Systems (CPS). While these systems open new opportunities to deliver improved quality of life for people and reinvigorate computing, their engineering is a difficult problem given the level of heterogeneity and dynamism they exhibit. While progress has been made, we argue that complexity is now at a level such that existing approaches need a major rethink to define principles and associated techniques for CPS. In this paper, we identify research challenges when modelling, analysing and engineering CPS. We focus on three key topics: theoretical foundations of CPS, self-adaptation methods for CPS, and exemplars of CPS serving as a research vehicle shared by a larger community. For each topic, we present an overview and suggest future research directions, thereby focusing on selected challenges. This paper is one of the results of the Shonan Seminar 118 on Modelling and Analysing Resilient Cyber-Physical Systems, which took place in December 2018.
- Published
- 2019
16. ATF7 mediates TNF-α-induced telomere shortening
- Author
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Bruno Chatton, Mami Yasukawa, Kenichi Nakamura, Manabu Koike, Toshio Maekawa, Daisuke Nakai, Keisuke Yoshida, Fuyuki Ishikawa, Kaiyo Takubo, Kenkichi Masutomi, Shunsuke Ishii, Binbin Liu, RIKEN BioResource Research Center [Tsukuba, Japan] (RIKEN BRC), National Cancer Center Research Institute [Tokyo], National Institutes for Quantum and Radiological Science and Technology (QST), Biotechnologie et signalisation cellulaire (BSC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS), and Kyoto University [Kyoto]
- Subjects
0301 basic medicine ,Telomerase ,p38 mitogen-activated protein kinases ,Biology ,Genome Integrity, Repair and Replication ,medicine.disease_cause ,Histones ,03 medical and health sciences ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Genetics ,medicine ,Psychological stress ,Animals ,Humans ,Phosphorylation ,Transcription factor ,Ku Autoantigen ,Telomere Shortening ,Mice, Knockout ,Tumor Necrosis Factor-alpha ,Chimie/Chimie organique ,Chromosome ,Fibroblasts ,Telomere ,Activating Transcription Factors ,Cell biology ,Mice, Inbred C57BL ,030104 developmental biology ,Psychosocial stress ,HeLa Cells - Abstract
Telomeres maintain the integrity of chromosome ends and telomere length is an important marker of aging. The epidemiological studies suggested that many types of stress including psychosocial stress decrease telomere length. However, it remains unknown how various stresses induce telomere shortening. Here, we report that the stress-responsive transcription factor ATF7 mediates TNF-α–induced telomere shortening. ATF7 and telomerase, an enzyme that elongates telomeres, are localized on telomeres via interactions with the Ku complex. In response to TNF-α, which is induced by various stresses including psychological stress, ATF7 was phosphorylated by p38, leading to the release of ATF7 and telomerase from telomeres. Thus, a decrease of ATF7 and telomerase on telomeres in response to stress causes telomere shortening, as observed in ATF7-deficient mice. These findings give credence to the idea that various types of stress might shorten telomere.
- Published
- 2018
17. Trustworthy Cyber-Physical Systems Engineering
- Author
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Alexander Romanovsky, Fuyuki Ishikawa, Alexander Romanovsky, and Fuyuki Ishikawa
- Subjects
- TJ213
- Abstract
From the Foreword'Getting CPS dependability right is essential to forming a solid foundation for a world that increasingly depends on such systems. This book represents the cutting edge of what we know about rigorous ways to ensure that our CPS designs are trustworthy. I recommend it to anyone who wants to get a deep look at these concepts that will form a cornerstone for future CPS designs.'--Phil Koopman, Carnegie Mellon University, Pittsburgh, Pennsylvania, USATrustworthy Cyber-Physical Systems Engineering provides practitioners and researchers with a comprehensive introduction to the area of trustworthy Cyber Physical Systems (CPS) engineering. Topics in this book cover questions such as What does having a trustworthy CPS actually mean for something as pervasive as a global-scale CPS? How does CPS trustworthiness map onto existing knowledge, and where do we need to know more? How can we mathematically prove timeliness, correctness, and other essential properties for systems that may be adaptive and even self-healing? How can we better represent the physical reality underlying real-world numeric quantities in the computing system? How can we establish, reason about, and ensure trust between CPS components that are designed, installed, maintained, and operated by different organizations, and which may never have really been intended to work together? Featuring contributions from leading international experts, the book contains sixteen self-contained chapters that analyze the challenges in developing trustworthy CPS, and identify important issues in developing engineering methods for CPS.The book addresses various issues contributing to trustworthiness complemented by contributions on TCSP roadmapping, taxonomy, and standardization, as well as experience in deploying advanced system engineering methods in industry. Specific approaches to ensuring trustworthiness, namely, proof and refinement, are covered, as well as engineering methods for dealing with hybrid aspects.
- Published
- 2017
18. Modelling and Analysing Resilient Cyber-Physical Systems.
- Author
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Bennaceur, Amel, Ghezzi, Carlo, Tei, Kenji, Kehrer, Timo, Weyns, Danny, Calinescu, Radu, Dustdar, Schahram, Zhenjiang Hu, Shinichi Honiden, Fuyuki Ishikawa, Zhi Jin, Kramer, Jeffrey, Litoiu, Marin, Loreti, Michele, Moreno, Gabriel A., Müller, Hausi A., Nenzi, Laura, Nuseibeh, Bashar, Pasquale, Liliana, and Reisig, Wolfgang
- Subjects
CYBER physical systems ,SELF-adaptive software ,SYSTEMS software ,MEDICAL equipment ,QUALITY of life ,INTELLIGENT buildings - Abstract
From smart buildings to medical devices to smart nations, software systems increasingly integrate computation, networking, and interaction with the physical environment. These systems are known as Cyber-Physical Systems (CPS). While these systems open new opportunities to deliver improved quality of life for people and reinvigorate computing, their engineering is a difficult problem given the level of heterogeneity and dynamism they exhibit. While progress has been made, we argue that complexity is now at a level such that existing approaches need a major re-think to define principles and associated techniques for CPS. In this paper, we identify research challenges when modelling, analysing and engineering CPS. We focus on three key topics: theoretical foundations of CPS, self-adaptation methods for CPS, and exemplars of CPS serving as a research vehicle shared by a larger community. For each topic, we present an overview and suggest future research directions, thereby focusing on selected challenges. This paper is one of the results of the Shonan Seminar 118 on Modelling and Analysing Resilient Cyber- Physical Systems, which took place in December 2018. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
19. Three-Dimensional Localization of an Individual Fluorescent Molecule with Angstrom Precision.
- Author
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Taku Furubayashi, Kazuya Motohashi, Keisuke Wakao, Tsuyoshi Matsuda, Isao Kii, Takamitsu Hosoya, Nobuhiro Hayashi, Mahito Sadaie, Fuyuki Ishikawa, Michio Matsushita, and Satoru Fujiyoshi
- Published
- 2017
- Full Text
- View/download PDF
20. Fission yeast Stn1 is crucial for semi-conservative replication at telomeres and subtelomeres.
- Author
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Masahiro Takikawa, Yusuke Tarumoto, and Fuyuki Ishikawa
- Published
- 2017
- Full Text
- View/download PDF
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