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Research Square 2021年

作者： Peng, Hanchuan Qu, Lei Li, Yuanyuan Xie, Peng Liu, Lijuan Wang, Yimin Wu, Jun Liu, Yu Wang, Tao Li, Longfei Guo, Kaixuan Wan, Wan ouyang, Lei Xiong, Feng Zheng, Yefeng Xu, Fang Gong, Hui Dong, Hongwei Luo, Qingming Bi, Guo-Qiang Hawrylycz, Michael Zeng, Hongkui Allen Institute for Brain Science United States Key Laboratory of Intelligent Computation & Signal Processing Ministry of Education Anhui University China SEU-ALLEN Joint Center Institute for Brain Intelligence Southeast University Bangladesh Institute for Brain and Intelligence Southeast University Bangladesh Tencent Jarvis Lab China CAS Key Laboratory of Brain Connectome and Manipulation China Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronics MoE Key Laboratory for Biomedical Photonics Huazhong University of Science and Technology China Center for Integrative Connectomics Department of Neurobiology David Geffen School of Medicine UCLA United States Hainan University China Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China China

Recent whole brain mapping projects are collecting large-scale 3D images using powerful and informative modalities, such as STPT, fMoST, VISoR, or MRI. Registration of these multi-dimensional whole-brain images onto a standard atlas is essential for characterizing neuron types and constructing brain wiring diagrams. However, cross-modality image registration is challenging due to intrinsic variations of brain anatomy and artifacts resulted from different sample preparation methods and imaging modalities. We introduced a cross-modality registration method, called mBrainAligner, which uses coherent landmark mapping as well as deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas. We also built a single cell resolution atlas using the fMoST modality, and used our method to generate whole brain map of 3D full single neuron morphology and neuron cell types. © 2021, CC BY.

关键词： Brain mapping

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New Framework for Code-Mapping-based Reversible Data Hiding in JPEG Images

arXiv

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arXiv 2020年

作者： Du, Yang Yin, Zhaoxia Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University Hefei230601 China Anhui Key Laboratory of Multimodal Cognitive Computation School of Computer Science and Technology Anhui University Hefei230601 China School of Communication & Electronic Engineering East China Normal University Shanghai200241 China

Code mapping (CM) is an efficient technique for reversible data hiding (RDH) in JPEG images, which embeds data by constructing a mapping relationship between the used and unused codes in the JPEG bitstream. This study presents a new framework for designing a CM-based RDH method. First, a new code mapping strategy is proposed to suppress file size expansion and improve applicability. Based on our proposed strategy, the mapped codes are redefined by creating a new Huffman table rather than selecting them from the unused codes in the original Huffman table. The critical issue of designing the CM-based RDH method, that is, constructing code mapping, is converted into a combinatorial optimization problem. This study proposes a novel CM-based RDH method that utilizes a genetic algorithm (GA). The experimental results demonstrate that the proposed method achieves a high embedding capacity with no signal distortion while suppressing file size expansion. Copyright © 2020, The Authors. All rights reserved.

关键词： Mapping

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Harmonized-Multinational qEEG norms (HarMNqEEG)

引用

NEURoIMAGE 2022年 256卷 119190-119190页

作者： Li, Min Wang, Ying Lopez-Naranjo, Carlos Hu, Shiang Reyes, Ronaldo Cesar Garcia Paz-Linares, Deirel Areces-Gonzalez, Ariosky Hamid, Aini Ismafairus Abd Evans, Alan C. Savostyanov, Alexander N. Calzada-Reyes, Ana Villringer, Arno Tobon-Quintero, Carlos A. Garcia-Agustin, Daysi Yao, Dezhong Dong, Li Aubert-Vazquez, Eduardo Reza, Faruque Razzaq, Fuleah Abdul omar, Hazim Abdullah, Jafri Malin Galler, Janina R. ochoa-Gomez, John F. Prichep, Leslie S. Galan-Garcia, Lidice Morales-Chacon, Lilia Valdes-Sosa, Mitchell J. Trondle, Marius Zulkifly, Mohd Faizal Mohd Rahman, Muhammad Riddha Bin Abdul Milakhina, Natalya S. Langer, Nicolas Rudych, Pavel Koenig, Thomas Virues-Alba, Trinidad A. Lei, Xu Bringas-Vega, Maria L. Bosch-Bayard, Jorge F. Valdes-Sosa, Pedro Antonio [a]The Clinical Hospital of Chengdu Brain Science Institute MOE Key Lab for Neuroinformation School of Life Science and Technology University of Electronic Science and Technology of China Chengdu China [b]Cuban Center for Neurocience La Habana Cuba [c]McGill Centre for Integrative Neuroscience Ludmer Centre for Neuroinformatics and Mental Health Montreal Neurological Institute Canada [d]Department of Neurosciences School of Medical Sciences Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [e]Brain and Behaviour Cluster School of Medical Sciences Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [f]Hospital Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [g]Humanitarian Institute Novosibirsk State University Novosibirsk 630090 Russia [h]Laboratory of Psychophysiology of Individual Differences Federal State Budgetary Scientific Institution Scientific Research Institute of Neurosciences and Medicine Novosibirsk 630117 Russia [i]Laboratory of Psychological Genetics at the Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences Novosibirsk 630090 Russia [j]University of Pinar del Río “Hermanos Saiz Montes de Oca” Pinar del Río Cuba [k]Department of Neurology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany [l]Department of Cognitive Neurology University Hospital Leipzig Leipzig Germany [m]Center for Stroke Research Charité-Universitätsmedizin Berlin Berlin Germany [n]Grupo Neuropsicología y Conducta - GRUNECO Faculty of Medicine Universidad de Antioquia Colombia [o]Research Department Institución Prestadora de Servicios de Salud IPS Universitaria Colombia [p]The Cuban center aging longevity and health Havana Cuba [q]Research Unit of NeuroInformation Chinese Academy of Medical Sciences Chengdu 2019RU035 China [r]School of Electrical Engineering Zhengzhou University Zhengzhou 4500

This paper extends frequency domain quantitative electroencephalography (qEEG) methods pursuing higher sensitivity to detect Brain Developmental Disorders. Prior qEEG work lacked integration of cross-spectral information omitting important functional connectivity descriptors. Lack of geographical diversity precluded accounting for site-specific variance, increasing qEEG nuisance variance. We ameliorate these weaknesses. (i) Create lifespan Riemannian multinational qEEG norms for cross-spectral tensors. These norms result from the HarMNqEEG project fostered by the Global Brain Consortium. We calculate the norms with data from 9 countries, 12 devices, and 14 studies, including 1564 subjects. Instead of raw data, only anonymized metadata and EEG cross spectral tensors were shared. After visual and automatic quality control, developmental equations for the mean and standard deviation of qEEG traditional and Riemannian DPs were calculated using additive mixed-effects models. We demonstrate qEEG "batch effects " and provide methods to calculate harmonized z-scores. (ii) We also show that harmonized Riemannian norms produce z-scores with increased diagnostic accuracy predicting brain dysfunction produced by malnutrition in the first year of life and detecting CoVID induced brain dysfunction. (iii) We offer open code and data to calculate different individual z-scores from the HarMNqEEG dataset. These results contribute to developing bias-free, low-cost neuroimaging technologies applicable in various health settings.

关键词： Quantitative EEG EEG cross-spectrum Riemannian geometry Batch effects Z-score Harmonization Malnutrition Covid induced brain dysfunction Developmental Brain Chart

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

arXiv

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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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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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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

引用

Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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Identification of pre-microRNAs by characterizing their sequence order evolution information and secondary structure graphs

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BMC bioinformatics 2018年第SUPPL 19期19卷 521页

作者： Yuanlin Ma Zuguo Yu Guosheng Han Jinyan Li Vo Anh Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan 411105 China. Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan 411105 China. yuzuguo@***. School of Electrical Engineering and Computer Science Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia. yuzuguo@***. Advanced Analytics Institute Faculty of Engineering & IT University of Technology Sydney P.O Box 123 Broadway NSW 2007 Australia. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia.

BACKGRoUND:Distinction between pre-microRNAs (precursor microRNAs) and length-similar pseudo pre-microRNAs can reveal more about the regulatory mechanism of RNA biological processes. Machine learning techniques have been widely applied to deal with this challenging problem. However, most of them mainly focus on secondary structure information of pre-microRNAs, while ignoring sequence-order information and sequence evolution information. RESULTS:We use new features for the machine learning algorithms to improve the classification performance by characterizing both sequence order evolution information and secondary structure graphs. We developed three steps to extract these features of pre-microRNAs. We first extract features from PSI-BLAST profiles and Hilbert-Huang transforms, which contain rich sequence evolution information and sequence-order information respectively. We then obtain properties of small molecular networks of pre-microRNAs, which contain refined secondary structure information. These structural features are carefully generated so that they can depict both global and local characteristics of pre-microRNAs. In total, our feature space covers 591 features. The maximum relevance and minimum redundancy (mRMR) feature selection method is adopted before support vector machine (SVM) is applied as our classifier. The constructed classification model is named MicroRNA -NHPred. The performance of MicroRNA -NHPred is high and stable, which is better than that of those state-of-the-art methods, achieving an accuracy of up to 94.83% on same benchmark datasets. CoNCLUSIoNS:The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the sequences and secondary structures, which are capable of characterizing the sequence evolution information and sequence-order information, and global and local information of pre-microRNAs secondary structures. MicroRNA -NHPred is a valuable method for pre-microRNAs iden

关键词： Hibert-Huang transform Network PSI-BLAST profiles Pre-microRNA SVM mRMR

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Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2024年第10期21卷 1959页

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Two weight Zpk -codes, p odd prime

arXiv

引用

arXiv 2017年

作者： Shi, Minjia Sepasdar, Zahra Solé, Patrick Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University No. 3 Feixi Road Hefei Anhui Province230039 China National Mobile Communications Research Laboratory Southeast University Nanjing210096 China School of Mathematical Sciences of Anhui University Hefei230601 China Department of Pure Mathematics Ferdowsi University of Mashhad P. O. Box 1159 Mashhad91775 Iran CNRS/LTCI Telecom ParisTech University of Paris-Saclay Paris75 013 France Department of Mathematics Faculty of Science King Abdulaziz University Jeddah21589 Saudi Arabia

We show that regular homogeneous two-weight Zpk -codes where p is odd and k ≥ 2 with dual Hamming distance at least four do not exist. The proof relies on existence conditions for the strongly regular graph built on ... 详细信息

关键词： Hamming distance

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Substrate integrated waveguide filter with improved stopband performance using LTCC technology

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Progress In Electromagnetics Research C 2014年 54卷 155-162页

作者： Zhang, Ping-Juan Li, Min-Quan College of Mathematics Physics and Information Engineering Anhui Science and Technology University Chuzhou233100 China Key Laboratory of Intelligent Computation and Signal Processing Ministry of Education Anhui University Hefei230039 China

A novel multi-layer third-order substrate integrated waveguide (SIW) bandpass filter with improved lower stopband performance is proposed. TE201-mode in folded-SIW cavity is utilized to implement negative cross coupling, and the TE101-mode is taken as a non-resonating node (NRN) for implementing bypass coupling. A circular aperture etched on the middle metal layer is used to realize coupling between source and the second SIW cavity. Then, three transmission zeros located below the passband can be obtained to improve stopband attenuation. Meanwhile, better spurious suppression performance above passband is achieved. A filter sample is designed and fabricated with multi-layer low-temperature co-fired ceramic (LTCC) technology. The measured S-parameters agree well with the simulated ones, with its predicted good performance. © 2014 Electromagnetics Academy. All rights reserved.

关键词： Substrate integrated waveguides

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