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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

Genomics, Proteomics & Bioinformatics 2020年第2期18卷 104-119页

作者： Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.G.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff Geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G.Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan Guo Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Westlake UniversityHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China School of Computer Science Shanghai Key Laboratory of Intelligent Information ProcessingFudan UniversityShanghai 200433China Thermo Fisher Scientific(BREMEN)GmbH Bremen 28195Germany OncoProteomics Laboratory Department of Medical OncologyVU University Medical CenterVU UniversityAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamUrologyCancer Center AmsterdamAmsterdam 1011The Netherlands Thermo Fisher Scientific Shanghai 201206China The Netherlands Cancer Institute Surgical OncologyAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamSurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPediatric Oncology/HematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamHematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamMedical OncologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamNeurosurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPathologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamOtolaryngology/Head and Neck SurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Erasmus MC University Medical Center PathologyRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center SurgeryRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center Medical OncologyRotterdam 1016LVThe Netherlands Department of Anatomical Pathology Singapore General HospitalSingapore 169608Singapore Division of Medical Scie

To address the increasing need for detecting and validating protein biomarkers in clinical specimens,mass spectrometry(MS)-based targeted proteomic techniques,including the selected reaction monitoring(SRM),parallel reaction monitoring(PRM),and massively parallel dataindependent acquisition(DIA),have been *** optimal performance,they require the fragment ion spectra of targeted peptides as prior *** this report,we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue *** build the spectral resource,we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on *** then applied the workflow to generate DPHL,a comprehensive DIA pan-human library,from 1096 data-dependent acquisition(DDA)MS raw files for 16 types of cancer *** extensive spectral resource was then applied to a proteomic study of 17 prostate cancer(PCa)***,PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was *** a second application,the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma(DLBCL)patients and 18 healthy control *** expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by *** data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker *** is freely accessible at https://***/page/***?id=IPX0001400000.

关键词： Data-independent acquisition Parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma

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Network Resilience

arXiv

引用

arXiv 2020年

作者： Liu, Xueming Li, Daqing Ma, Manqing Szymanski, Boleslaw K. Eugene Stanley, H. Gao, Jianxi Key Laboratory of Image Information Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Hubei Wuhan430074 China School of Reliability and Systems Engineering Beihang University Beijing100191 China College of Safety Science and Engineering Civil Aviation University of China Tianjin 300300 China Department of Computer Science Rensselaer Polytechnic Institute TroyNY12180 United States Network Science and Technology Center Rensselaer Polytechnic Institute TroyNY12180 United States Center for Polymer Studies Department of Physics Boston University BostonMA02215 United States

Many systems on our planet shift abruptly and irreversibly from the desired state to an undesired state when forced across a "tipping point". Some examples are mass extinctions within ecosystems, cascading failures in infrastructure systems, and changes in human and animal social networks. The ability to avoid such regime shifts or to recover quickly from such a non-resilient state demonstrates a system's resilience;system resilience is a quality that enables a system to adjust its activities to retain its basic functionality when errors and failures occur. In the past 50 years, attention has been paid almost exclusively to low-dimensional systems;scholars have focused on the calibration of the resilience functions of such systems and the identification of indicators of early warning signals based on two to three connected components. In recent years, taking advantage of network theory and the availability of lavish real datasets, network scientists have begun to explore real-world complex networked multidimensional systems, as well as their resilience functions and early warning indicators. This report presents a comprehensive review of resilience functions and regime shifts in complex systems in domains such as ecology, biology, society, and infrastructure. The research approach includes empirical observations, experimental studies, mathematical modeling, and theoretical analysis. We also review the definitions of some ambiguous terms, including robustness, resilience, and stability. Copyright © 2020, The Authors. All rights reserved.

关键词： Complex networks

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Corrigendum to a Low-Cost, Light-Weight Climbing Robot for Inspection of Glass Curtains

引用

International Journal of advanced Robotic systems 2015年第3期12卷 20-20页

作者： Ran Liang Meteb Altaf Eball Ahmad Rong Liu Ke Wang Robotics Institute School of Mechanical Engineering and Automation Beihang University Beijing China National Robotics & Intelligent Systems center King AbdulAziz City for Science and Technology Saudi Arabia Riyadh Saudi Arabia Arts et Métiers ParisTech Design Manufacturing and Control Laboratory (LCFC) Paris France

Corrigendum, corrigendum

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Tiny noise, big mistakes: Adversarial perturbations induce errors in Brain-Computer Interface spellers

arXiv

引用

arXiv 2020年

作者： Zhang, Xiao Wu, Dongrui Ding, Lieyun Luo, Hanbin Lin, Chin-Teng Jung, Tzyy-Ping Chavarriaga, Ricardo Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China School of Civil Engineering and Mechanics Huazhong University of Science and Technology Wuhan430074 China Centre of Artificial Intelligence Faculty of Engineering and Information Technology University of Technology Sydney Sydney2007 Australia La Jolla CA92093 United States Center for Advanced Neurological Engineering Institute of Engineering in Medicine UCSD La Jolla CA92093 United States ZHAW DataLab Zürich University of Applied Sciences Winterthur8401 Switzerland

An electroencephalogram (EEG) based brain-computer interface (BCI) speller allows a user to input text to a computer by thought. It is particularly useful to severely disabled individuals, e.g., amyotrophic lateral sclerosis patients, who have no other effective means of communication with another person or a computer. Most studies so far focused on making EEG-based BCI spellers faster and more reliable;however, few have considered their security. This study, for the first time, shows that P300 and steady-state visual evoked potential BCI spellers are very vulnerable, i.e., they can be severely attacked by adversarial perturbations, which are too tiny to be noticed when added to EEG signals, but can mislead the spellers to spell anything the attacker wants. The consequence could range from merely user frustration to severe misdiagnosis in clinical applications. We hope our research can attract more attention to the security of EEG-based BCI spellers, and more broadly, EEG-based BCIs, which has received little attention before. Copyright © 2020, The Authors. All rights reserved.

关键词： Electroencephalography

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Holographic MIMO Communications with Arbitrary Surface Placements: Near-Field LoS Channel Model and Capacity Limit

arXiv

引用

arXiv 2023年

作者： Gong, Tierui Wei, Li Huang, Chongwen Yang, Zhijia He, Jiguang Debbah, Mérouane Yuen, Chau School of Electrical and Electronics Engineering Nanyang Technological University Singapore639798 Singapore College of Information Science and Electronic Engineering Zhejiang University Hangzhou310027 China Hangzhou310027 China State Key Laboratory of Robotics Shenyang Institute of Automation Chinese Academy of Sciences Shenyang110016 China Key Laboratory of Networked Control Systems Chinese Academy of Sciences Shenyang110016 China Institutes for Robotics and Intelligent Manufacturing Chinese Academy of Sciences Shenyang110169 China Technology Innovation Institute Masdar City Abu Dhabi9639 United Arab Emirates KU 6G Research Center Khalifa University of Science and Technology P O Box 127788 Abu Dhabi United Arab Emirates CentraleSupelec University Paris-Saclay Gif-sur-Yvette91192 France

Envisioned as one of the most promising technologies, holographic multiple-input multiple-output (H-MIMO) recently attracts notable research interests for its great potential in expanding wireless possibilities and achieving fundamental wireless limits. Empowered by the nearly continuous, large and energy-efficient surfaces with powerful electromagnetic (EM) wave control capabilities, H-MIMO opens up the opportunity for signal processing in a more fundamental EM-domain, paving the way for realizing holographic imaging level communications in supporting the extremely high spectral efficiency and energy efficiency in future networks. In this article, we propose a generalized EM-domain near-field channel modeling and study its capacity limit of point-to-point H-MIMO systems that equips arbitrarily placed surfaces in a line-of-sight (LoS) environment. Two effective and computational-efficient channel models are established from their integral counterpart, where one is with a sophisticated formula but showcases more accurate, and another is concise with a slight precision sacrifice. Furthermore, we unveil the capacity limit using our channel model, and derive a tight upper bound based upon an elaborately built analytical framework. Our result reveals that the capacity limit grows logarithmically with the product of transmit element area, receive element area, and the combined effects of 1/d2mn, 1/d4mn, and 1/d6mn over all transmit and receive antenna elements, where dmn indicates the distance between each transmit element n and receive element m. Particularly, 1/d6mn dominates in the near-field region whereas 1/d2mn dominates in the far-field region. Numerical evaluations validate the effectiveness of our channel models, and showcase the slight disparity between the upper bound and the exact capacity, which is beneficial for predicting practical system performance. Copyright © 2023, The Authors. All rights reserved.

关键词： MIMO systems

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Privacy-Preserving Brain-Computer Interfaces: A Systematic Review

arXiv

引用

arXiv 2024年

作者： Xia, Kun Duch, Wlodzislaw Sun, Yu Xu, Kedi Fang, Weili Luo, Hanbin Zhang, Yi Sang, Dong Xu, Xiaodong Wang, Fei-Yue Wu, Dongrui The Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China Zhejiang Lab Hangzhou311121 China The Department of Informatics School of Physics Astronomy and Informatics Neurocognitive Laboratory Center for Modern Interdisciplinary Technologies Nicolaus Copernicus University Torun Poland The Ministry of Education Key Laboratory for Biomedical Engineering Zhejiang University Hangzhou China The Zhejiang University School of Medicine National Clinical Research Center for Child Health Hangzhou China Department of Biomedical Engineering Zhejiang University Hangzhou China The School of Civil and Hydraulic Engineering Huazhong University of Science and Technology Wuhan430074 China The College of Public Administration Huazhong University of Science and Technology Wuhan430074 China The NetsUnion Clearing Corporation Beijing100045 China The State Key Laboratory for Management and Control of Complex Systems Institute of Automation Chinese Academy of Sciences Beijing100049 China

A brain-computer interface (BCI) establishes a direct communication pathway between the human brain and a computer. It has been widely used in medical diagnosis, rehabilitation, education, entertainment, etc. Most research so far focuses on making BCIs more accurate and reliable, but much less attention has been paid to their privacy. Developing a commercial BCI system usually requires close collaborations among multiple organizations, e.g., hospitals, universities, and/or companies. Input data in BCIs, e.g., electroencephalogram (EEG), contain rich privacy information, and the developed machine learning model is usually proprietary. Data and model transmission among different parties may incur significant privacy threats, and hence privacy protection in BCIs must be considered. Unfortunately, there does not exist any contemporary and comprehensive review on privacy-preserving BCIs. This paper fills this gap, by describing potential privacy threats and protection strategies in BCIs. It also points out several challenges and future research directions in developing privacy-preserving BCIs. © 2024, CC BY.

关键词： Differential privacy

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An Early Stage Researcher's Primer on systems Medicine Terminology

Network and Systems Medicine

引用

Network and systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

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Fabrication of translucent graded dental crown using zirconia-yttrium multi-slurry tape casting 3D printer

引用

Journal of the Mechanical Behavior of Biomedical Materials 2024年 152卷 106406页

作者： Romario, Yulius Shan Bhat, Chinmai Ramezani, Maziar Pasang, Tim Chen, Zhangwei Jiang, Cho-Pei Graduate Institute of Manufacturing Technology National Taipei University of Technology 1 Sec. 3 Zhongxiao E. Rd. Taipei10608 Taiwan High-value Biomaterials Research and Commercialization Center National Taipei University of Technology 1 Sec. 3 Zhongxiao E. Rd. Taipei10608 Taiwan Department of Mechanical Engineering Auckland University of Technology Auckland1010 New Zealand Department of Engineering Design Manufacturing and Management Systems Western Michigan University KalamazooMI4900-5200 United States Additive Manufacturing Institute Shenzhen University Shenzhen518060 China Guangdong Key Laboratory of Electromagnetic Control and Intelligent Robotics College of Mechatronics and Control Engineering Shenzhen University Shenzhen518060 China Department of Mechanical Engineering National Taipei University of Technology 1 Sec. 3 Zhongxiao E. Rd. Taipei10608 Taiwan

This paper aims to fabricate functionally graded dental crown using a multi-slurry tape casting additive manufacturing technology. The different luminescence of the dental crown was obtained with different composition of zirconia and yttria. Zirconia with tunable mechanical properties and translucency are obtained by adding 3, 3.5, 4, 4.5, and 5 mol% of yttrium oxide to zirconia powder. After obtaining the printable slurry with maximum solid loading, the green bodies are prepared using the in-house built high-speed multi-ceramic tape casting technology. They are later sintered with two-stage sintering method. After the successful fabrication, the mechanical properties and translucency of the specimens were evaluated with Vickers hardness, three-point bending and translucency parameter tests. Finally, an FGM tooth crown with five photocurable slurries is proposed to demonstrate the translucent gradient effect of sintered part. The solid loading of 80% zirconia and 20% resin delivered samples without any surface cracks. The shrinkage ratio analysis showed that the sintered sample dimension was reduced by 20%, 20%, and 23% along X, Y, and Z directions. The samples fabricated with 3% yttrium oxide to zirconia delivered excellent hardness (1687 HV) and flexural strength (650.6 MPa). However, the relative luminescence increased with increasing the yttrium oxide for 3–5 mol%. With the optimized process parameters, the proposed dental crown is fabricated and analyzed for their shrinkage ratio, mechanical, and translucency properties. The study proposes the potential of fabricating customized dental crown with gradient translucent appearance. © 2024

关键词： Zirconia

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Fabrication of Translucent Graded Dental Crown Using Zirconia-Yttrium Multi-Slurry Tape Casting 3d Printer

SSRN

引用

SSRN 2024年

This paper aims to fabricate functionally graded dental crown using a multi-slurry tape casting additive manufacturing technology. The different luminescence of the dental crown was obtained with different composition of zirconia and yttria. Zirconia with tunable mechanical properties and translucency are obtained by adding 3, 3.5, 4, 4.5, and 5 mol% of yttrium oxide to zirconia powder. After obtaining the printable slurry with maximum solid loading, the green bodies are prepared using the in-house built high speed multi-ceramic tape casting technology. They are later sintered with two-stage sintering method. After the successful fabrication, the mechanical properties and translucency of the specimens were evaluated with Vickers hardness, three-point bending and translucency parameter tests. Finally, an FGM tooth crown with five photocurable slurries is proposed to demonstrate the translucent gradient effect of sintered part. The solid loading of 80% zirconia and 20% resin delivered samples without any surface cracks. The shrinkage ratio analysis showed that the sintered sample dimension was reduced by 20%, 20%, and 23% along X, Y, and Z directions. The samples fabricated with 3% yttrium oxide to zirconia delivered excellent hardness (1687 HV) and flexural strength (650.6 MPa). However, the relative luminescence increased with increasing the yttrium oxide for 3 – 5 mol%. With the optimized process parameters, the proposed dental crown is fabricated and analyzed for their shrinkage ratio, mechanical, and translucency properties. The study proposes the potential of fabricating customized dental crown with gradient translucent appearance. © 2024, The Authors. All rights reserved.

关键词： Zirconia

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Spike-burst chimera states in an adaptive exponential integrate-and-fire neuronal network

arXiv

引用

arXiv 2019年

作者： Santos, Moises S. Protachevicz, Paulo R. Iarosz, Kelly C. Caldas, Iberê L. Viana, Ricardo L. Borges, Fernando S. Ren, Hai-Peng Szezech, José D. Batista, Antonio M. Grebogi, Celso Department of Physics Federal University of Paraná CuritibaPR80060-000 Brazil Graduate in Science Program - Physics State University of Ponta Grossa Ponta Grossa PR84030-900 Brazil Institute of Physics University of São Paulo São PauloSP05508-900 Brazil Center for Mathematics Computation and Cognition Federal University of ABC São Bernardo do CampoSP09606-045 Brazil Shaanxi Key Laboratory of Complex System Control and Intelligent Information Processing Xian University of Technology Xi'an710048 China Xian Technological University Xi'an710021 China Graduate in Science Program - Physics State University of Ponta Grossa Ponta Grossa PR84030-900 Brazil Institute for Complex Systems and Mathematical Biology King's College University of Aberdeen AberdeenAB24 3UE United Kingdom

Chimera states are spatiotemporal patterns in which coherence and incoherence coexist. We observe the coexistence of synchronous (coherent) and desynchronous (incoherent) domains in a neuronal network. The network is composed of coupled adaptive exponential integrate-and-fire neurons that are connected by means of chemical synapses. In our neuronal network, the chimera states exhibit spatial structures both with spikes and bursts activities. Furthermore, those desynchronised domains not only have either spike or burst activity, but we show that the structures switch between spikes and bursts as the time evolves. Moreover, we verify the existence of multicluster chimera states. Copyright © 2019, The Authors. All rights reserved.

关键词： Neural networks

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