Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes

Renier, Nicolas, Adams, Eliza L., Kirst, Christoph, Wu, Zhuhao, Azevedo, Ricardo, Kohl, Johannes, Autry, Anita E., Kadiri, Lolahon +8 more·2016·Cell

DOI 10.1016/j.cell.2016.05.007

Cited by (922)

Items 201–300 of 922

Virtual reality-empowered deep-learning analysis of brain cells
Kaltenecker, Doris, Al-Maskari, Rami, Negwer, Moritz, Hoeher, Luciano, Kofler, Florian, Zhao, Shan, Todorov, Mihail, Rong, Zhouyi, Paetzold, Johannes Christian, Wiestler, Benedikt et al. · 2024 · Nature Methods
A tridimensional atlas of the developing human head
Blain, Raphael, Couly, Gérard, Shotar, Eimad, Blévinal, Joséphine, Toupin, Maryne, Favre, Anais, Abjaghou, Ali, Inoue, Megumi, Hernández-Garzón, Edwin, Clarençon, Frédéric et al. · 2023 · Cell
GLP-1 and nicotine combination therapy engages hypothalamic and mesolimbic pathways to reverse obesity
Sarah Falk, Jonas Petersen, Charlotte Svendsen, César Ramón Romero Leguizamón, Søren H. Jørgensen, Nathalie Krauth, Mette Q. Ludwig, Kathrine Lundø, Urmas Roostalu, Grethe Skovbjerg et al. · 2023 · Cell Reports
Comparative analysis reveals Ce3D as optimal clearing method for in toto imaging of the mouse intestine
Gleison Daion Piovezana Bossolani, Isabel Pintelon, Jan R. Detrez, Roeland Buckinx, Sofie Thys, Jacqueline Nelisis Zanoni, Winnok Harald De Vos, Jean‐Pierre Timmermans · 2019 · Neurogastroenterology & Motility
Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies
Nobuyuki Tanaka, Shigeaki Kanatani, Dagmara Kaczyńska, Keishiro Fukumoto, Lauri M. Louhivuori, Tomohiro Mizutani, Oded Kopper, Pauliina Kronqvist, Stephanie Robertson, Claes Lindh et al. · 2020 · Nature Biomedical Engineering
Terrain deformation measurements from optical satellite imagery: The MPIC-OPT processing services for geohazards monitoring
Floriane Provost, David Michéa B, Jean‐Philippe Malet, Enguerran Boissier, Elisabeth Pointal, André Stumpf, Fabrizio Pacini, Marie‐Pierre Doin, Pascal Lacroix, Catherine Proy et al. · 2022 · Remote Sensing of Environment
Input-dependent segregation of visual and somatosensory circuits in the mouse superior colliculus
Teresa Guillamón-Vivancos, Mar Aníbal-Martínez, Lorenzo Puche-Aroca, Juan Antonio Moreno‐Bravo, Miguel Valdeolmillos, Francisco J. Martini, Guillermina López‐Bendito · 2022 · Science
Efficient 3D light-sheet imaging of very large-scale optically cleared human brain and prostate tissue samples
Anna Schueth, Sven Hildebrand, Iryna V. Samarska, Shubharthi Sengupta, Annemarie Kiessling, Andreas Herrler, Axel zur Hausen, Michael Capalbo, Alard F. Roebroeck · 2023 · Communications Biology
D-LMBmap: a fully automated deep-learning pipeline for whole-brain profiling of neural circuitry
Zhongyu Li, Zengyi Shang, Jingyi Liu, Haotian Zhen, Entao Zhu, Shilin Zhong, Robyn N. Sturgess, Yitian Zhou, Xuemeng Hu, Xingyue Zhao et al. · 2023 · Nature Methods
Deep 3D histology powered by tissue clearing, omics and AI
Ali Ertürk · 2024 · Nature Methods
Differential fear conditioning generates prefrontal neural ensembles of safety signals
Alex Corches, Alex Hiroto, Tyler W. Bailey, John H. Speigel, Justin Pastore, Mark R. Mayford, Edward Korzus · 2018 · Behavioural Brain Research
Whole mouse brain reconstruction and registration to a reference atlas with standard histochemical processing of coronal sections
Brian S. Eastwood, Bryan M. Hooks, Ronald F. Paletzki, Nathan O’Connor, Jacob R. Glaser, Charles R. Gerfen · 2018 · The Journal of Comparative Neurology
Deep learning in biomedical image analysis
Minjeong Kim, Chenggang Clarence Yan, Defu Yang, Qian Wang, Junbo Ma, Guorong Wu A · 2019 · Elsevier eBooks
Specification of oxytocinergic and vasopressinergic circuits in the developing mouse brain
M. Pilar Madrigal, Sandra Jurado · 2021 · Communications Biology
Overactivation of GnRH neurons is sufficient to trigger polycystic ovary syndrome-like traits in female mice
Mauro S. B. Silva, Laurine Decoster, Gaspard Delpouve, Tori Lhomme, Gaëtan Ternier, Vincent Prévot, Paolo Giacobini · 2023 · EBioMedicine
BMP9 signaling promotes the normalization of tumor blood vessels
Claire Viallard, Cindy Audiger, Natalija Popović, Naoufal Akla, Kevin Lanthier, Isaac Legault-Navarrete, Heather J. Melichar, Santiago Costantino, Sylvie Lesage, Bruno Larrivée · 2020 · Oncogene
Ecotype differences in aggression, neural activity and behaviorally relevant gene expression in cichlid fish
Nicole M. Baran, Jeffrey Todd Streelman · 2020 · Genes Brain & Behavior
Identification of the suprachiasmatic nucleus venous portal system in the mammalian brain
Yifan Yao, Alana Taub, Joseph LeSauter, Rae Silver · 2021 · Nature Communications
Brain-wide mapping of contextual fear memory engram ensembles supports the dispersed engram complex hypothesis
Dheeraj S. Roy, Young-Gyun Park, Sachie K. Ogawa, Jae H. Cho, Heejin Choi, Lee Kamensky, Jared Martin, Kwanghun Chung, Susumu Tonegawa · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
Protracted neuronal recruitment in the temporal lobes of young children
M. A. Nascimento, S. Biagiotti, V. Herranz-Pérez, Samara Santiago, Raymund Bueno, C. Ye, Taylor J. Abel, Zhuang-Zhi Zhang, Juan S. Rubio-Moll, A. Kriegstein et al. · 2023 · Nature
A mutant with bilateral whisker to barrel inputs unveils somatosensory mapping rules in the cerebral cortex
Nicolas Renier, Chloé Dominici, Reha S. Erzurumlu, Claudius F. Kratochwil, Filippo M. Rijli, Patrícia Gaspar, Alain Chédotal · 2017 · eLife
Pathways to clinical CLARITY: volumetric analysis of irregular, soft, and heterogeneous tissues in development and disease
Brian Hsueh, Vanessa M. Burns, P. Pauerstein, Katherine M. Holzem, Li Ye, K. Engberg, Ai-Chi Wang, Xue-Ying Gu, Harini Chakravarthy, H. Arda et al. · 2017 · Scientific Reports
Tissue Clearing and Expansion Methods for Imaging Brain Pathology in Neurodegeneration: From Circuits to Synapses and Beyond
Arnaldo Parra‐Damas, Carlos A. Saura · 2020 · Frontiers in Neuroscience
High-resolution confocal and light-sheet imaging of collagen 3D network architecture in very large samples
Grigorii Timin, Michel C. Milinkovitch · 2023 · iScience
Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain
David Matthew Young, Siavash Fazel Darbandi, Grace Schwartz, Zachary Bonzell, Deniz Yuruk, Mai Nojima, Laurent Golé, John L.R. Rubenstein, Weimiao Yu, Stephan Sanders · 2021 · eLife
Continuous subcellular resolution three-dimensional imaging on intact macaque brain
Can Zhou, Xiaoquan Yang, Shihao Wu, Qiuyuan Zhong, Ting Luo, Anan Li, Guangcai Liu, Qingtao Sun, Pan Luo, Lei Deng et al. · 2021 · 中国科学通报：英文版
Brain-wide reconstruction of inhibitory circuits after traumatic brain injury
Jan C. Frankowski, Alexa Marie Tierno, Shreya Pavani, Quincy Cao, David C. Lyon, Robert F. Hunt · 2022 · Nature Communications
Light sheet fluorescence microscopy as a new method for unbiased three-dimensional analysis of vascular injury
Nicholas E. Buglak, Jennifer L. Lucitti, Pablo Ariel, Sophie L. Maiocchi, Francis J. Miller, Edward Moreira Bahnson · 2020 · Cardiovascular Research
Revisiting the role of Dcc in visual system development with a novel eye clearing method
Robin J. Vigouroux, Quénol Cesar, Alain Chédotal, Kim Tuyen Nguyen-Ba-Charvet · 2020 · eLife
Dosage-sensitive genes in autism spectrum disorders: From neurobiology to therapy
Sehrish Javed, Tharushan Selliah, Yu‐Ju Lee, Wei‐Hsiang Huang · 2020 · Neuroscience & Biobehavioral Reviews
Structural and functional imaging of brains
Zhichao Liu, Ying Jie Zhu, Liming Zhang, Weiping Jiang, Yawei Liu, Qiaowei Tang, Xiaoqing Cai, Jiang Li, Lihua Wang, Chang-Lu Tao et al. · 2022 · Science China Chemistry
Estradiol-mediated protection against high-fat diet induced anxiety and obesity is associated with changes in the gut microbiota in female mice
Kalpana D. Acharya, Madeline Graham, Harshini Raman, Abigail E. R. Parakoyi, A. Corcoran, M. Belete, B. Ramaswamy, Shashikant Koul, I. Sachar, Kevin Derendorf et al. · 2023 · Scientific Reports
An active texture-based digital atlas enables automated mapping of structures and markers across brains
Yuncong Chen, Lauren E. McElvain, Alexander S. Tolpygo, Daniel D. Ferrante, Beth Friedman, Partha P. Mitra, Harvey J. Karten, Yoav Freund, David Kleinfeld · 2019 · Nature Methods
On the Usage of Brain Atlases in Neuroimaging Research
Hess, Andreas, Hinz, Rukun, Keliris, Georgios A., Boehm-Sturm, Philipp · 2018 · Molecular Imaging and Biology
Incubation of palatable food craving is associated with brain-wide neuronal activation in mice
Rajtarun Madangopal, Eric R Szelenyi, Joseph Dan Khoa Nguyen, Megan B. Brenner, Olivia R. Drake, Diana Q. Pham, Aniruddha Shekara, Michelle Jin, Jia Jie Choong, Conor Heins et al. · 2022 · Proceedings of the National Academy of Sciences
Photostimulation of lymphatic clearance of β-amyloid from mouse brain: a new strategy for the therapy of Alzheimer’s disease
Dongyu Li, Hao Ran Lin, Silin Sun, Shaojun Liu, Zhang Liu, Yuening He, Jingtan Zhu, Jianyi Xu, OXANA V. SEMYACHKINA-GLUSHKOVSKAYA, Tingting Yu et al. · 2023 · Frontiers of Optoelectronics
Heightened lateral habenula activity during stress produces brainwide and behavioral substrates of susceptibility
Anna Zhukovskaya, Christopher A Zimmerman, Lindsay Willmore, Alejandro Pan-Vazquez, Sanjeev R. Janarthanan, Laura A. Lynch, Annegret L. Falkner, Ilana B. Witten · 2024 · Neuron
Illuminating the Activated Brain: Emerging Activity-Dependent Tools to Capture and Control Functional Neural Circuits
Qiye He, Jihua Wang, Hailan Hu · 2018 · Neuroscience Bulletin
Single-cell memory trace imaging with immediate-early genes
Magdalena M. Sauvage, Takashi Kitsukawa, Erika Atucha · 2019 · Journal of Neuroscience Methods
Characterization of the Brain Functional Architecture of Psychostimulant Withdrawal Using Single-Cell Whole-Brain Imaging
Adam Kimbrough, Lauren C. Smith, Marsida Kallupi, Sierra Simpson, Andrés Collazo, Olivier George · 2021 · eNeuro
Cerebellar contributions to a brainwide network for flexible behavior in mice
Jessica L. Verpeut, Silke Bergeler, Mikhail Kislin, F. William Townes, Ugne Klibaite, Zahra M. Dhanerawala, Austin Hoag, Sanjeev R. Janarthanan, Caroline Jung, Junuk Lee et al. · 2023 · Communications Biology
Whole-Brain Microscopy Meets In Vivo Neuroimaging: Techniques, Benefits, and Limitations
M. Aswendt, M. Schwarz, W. Abdelmoula, J. Dijkstra, S. Dedeurwaerdere · 2017 · Molecular Imaging and Biology
Network models to enhance the translational impact of cross-species studies
Julia K. Brynildsen, Kanaka Rajan, Michael X. Henderson, Dani S. Bassett · 2023 · Nature reviews. Neuroscience
Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture
Madison R. Glass, Elisa A. Waxman, Satoshi Yamashita, Michael J. Lafferty, Alvaro A. Beltran, Tala M. Farah, Niyanta K Patel, Rubal Singla, Nana Matoba, Sara M. Ahmed et al. · 2024 · Stem Cell Reports
Ca2+-binding protein NECAB2 facilitates inflammatory pain hypersensitivity
Ming-Dong Zhang, Jie Su, Csaba Ádori, Valentina Cinquina, Katarzyna Maleńczyk, Fatima Girach, Changgeng Peng, Patrik Ernfors, Peter Löw, Lotta Borgius et al. · 2018 · Journal of Clinical Investigation
Elimination of fibrin γ-chain cross-linking by FXIIIa increases pulmonary embolism arising from murine inferior vena cava thrombi
Cédric Duval, Adomas Baranauskas, Tímea Feller, Majid Ali, Lih T. Cheah, Nadira Y. Yuldasheva, Stephen R. Baker, Helen R. McPherson, Zaher Raslan, Marc Bailey et al. · 2021 · Proceedings of the National Academy of Sciences
A fast, aqueous, reversible three-day tissue clearing method for adult and embryonic mouse brain and whole body
Stylianos Kosmidis, Adrian Negrean, Alex Dranovsky, Attila Losonczy, Eric R. Kandel · 2021 · Cell Reports Methods
Nanoscale resolution imaging of the whole mouse embryos and larval zebrafish using expansion microscopy
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Molecular recording of calcium signals via calcium-dependent proximity labeling
Jungwoo Wren Kim, Adeline J. H. Yong, Erin E. Aisenberg, Joseph H. Lobel, Wei Wang, Ted M. Dawson, Valina Lynn Dawson, Ruixuan Gao, Lily Yeh Jan, Helen S. Bateup et al. · 2024 · Nature Chemical Biology
3D Visualization of the Temporal and Spatial Spread of Tau Pathology Reveals Extensive Sites of Tau Accumulation Associated with Neuronal Loss and Recognition Memory Deficit in Aged Tau Transgenic Mice
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Optimization of immunolabeling and clearing techniques for indelibly labeled memory traces
Ina P. Pavlova, Shannon C. Shipley, Marcos Lanio, René Hen, Christine Ann Denny · 2018 · Hippocampus
iDISCO+ for the Study of Neuroimmune Architecture of the Rat Auditory Brainstem
Paola Perin, Fabian F. Voigt, Philipp Bethge, Fritjof Helmchen, Roberto Pizzala · 2019 · Frontiers in Neuroanatomy
Parenting — a paradigm for investigating the neural circuit basis of behavior
Johannes Kohl · 2019 · Current Opinion in Neurobiology
Organic solvent‐based tissue clearing techniques and their applications
Yanjing Zhan, Haoyan Wu, Linfeng Liu, Jie Lin, Shiwen Zhang · 2021 · Journal of Biophotonics
Three-Dimensional Imaging Provides Detailed Atherosclerotic Plaque Morphology and Reveals Angiogenesis After Carotid Artery Ligation
Tobias Becher, Dario F. Riascos‐Bernal, Daniel J. Kramer, Vanessa M. Almonte, Jingyi Chi, Tao Tong, Gustavo Henrique Oliveira‐Paula, Issam Koleilat, Wei Chen, Paul Cohen et al. · 2020 · Circulation Research
Global brain c-Fos profiling reveals major functional brain networks rearrangements after alcohol reexposure
Marzena Stefaniuk, Monika Pawłowska, Marcin Barański, Klaudia Nowicka, Zbigniew Zieliński, Łukasz Bijoch, Diana Legutko, Piotr Majka, Sylwia Bednarek, Natalia Jermakow et al. · 2023 · Neurobiology of Disease
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Jenny Thai, John‐Paul Fuller‐Jackson, Jason J. Ivanusic · 2024 · The Journal of Comparative Neurology
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Minsuk Hyun, Julián Taranda, Gianna Radeljic, Lauren E. Miner, Wengang Wang, Nicole E. Ochandarena, Kee Wui Huang, Pavel Osten, Bernardo Luis Sabatini · 2020 · Proceedings of the National Academy of Sciences
SMART: An Open-Source Extension of WholeBrain for Intact Mouse Brain Registration and Segmentation
Michelle Jin, Joseph D. Nguyen, Sophia J. Weber, Carlos A. Mejias-Aponte, Rajtarun Madangopal, Sam A. Golden · 2022 · eNeuro
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Suhaas Anbazhakan, Pamela E. Rios Coronado, Ana Natalia L. Sy-Quia, Lek Wei Seow, Aubrey M. Hands, Mingming Zhao, Melody L. Dong, Martin R. Pfaller, Zhainib Adel Amir, Brian C. Raftrey et al. · 2022 · Nature Cardiovascular Research
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Tao Jiang, Ben Long, Hui Gong, Tonghui Xu, Xiangning Li, Zhuonan Duan, Anan Li, Lei Deng, Qiuyuan Zhong, Xue Peng et al. · 2017 · Scientific Reports
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Neural control of sexually dimorphic social behaviors
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Macrophage-B Cell Interactions in the Inverted Porcine Lymph Node and Their Response to Porcine Reproductive and Respiratory Syndrome Virus
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Segmentor: a tool for manual refinement of 3D microscopy annotations
David Borland, Carolyn M. McCormick, Niyanta K Patel, Oleh Krupa, Jessica T. Mory, Alvaro A. Beltran, Tala M. Farah, Carla F. Escobar-Tomlienovich, Sydney S. Olson, Minjeong Kim et al. · 2021 · BMC Bioinformatics
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Review of micro-optical sectioning tomography (MOST): technology and applications for whole-brain optical imaging [Invited]
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Bi-channel image registration and deep-learning segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain
Xuechun Wang, Weilin Zeng, Xiaodan Yang, Yong-Sheng Zhang, Chunyu Fang, Shaoqun Zeng, Yunyun Han, Peng Fei · 2021 · eLife
Tissue Clearing and Light Sheet Microscopy: Imaging the Unsectioned Adult Zebra Finch Brain at Cellular Resolution
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Tissue optical clearing for 3D visualization of vascular networks: A review
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Tao Jiang, Hui Gong, Jing Yuan · 2023 · Neuroscience Bulletin
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Hatylas F. Z de Azevedo, Marcos Antonio Ferreira, Alessandra Mascarello, Pavel Osten, Cristiano R. W. Guimarães · 2020 · Neurobiology of Stress
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Alessandra Franceschini, Giacomo Mazzamuto, Curzio Checcucci, Lorenzo Chicchi, Duccio Fanelli, Irene Costantini, Maria Beatrice Passani, Bianca A. Silva, Francesco Saverio Pavone, Ludovico Silvestri · 2023 · Cell Reports
Enkephalin-producing regulatory T cells in the skin restrain local inflammation through control of nociception
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Tissue Clearing and Deep Imaging of the Kidney Using Confocal and Two-Photon Microscopy
Daniyal J. Jafree, David Andrew Long, Peter James Scambler, DALE A. MOULDING · 2019 · Methods in molecular biology
Repetitive non-invasive prefrontal stimulation reverses neuropathic pain via neural remodelling in mice
Zheng Gan, Han Li, Paul Vincent Naser, Yechao Han, Linette Liqi Tan, Manfred Josef Oswald, Rohini Kuner · 2021 · Progress in Neurobiology
Suppression of neuropathic pain and comorbidities by recurrent cycles of repetitive transcranial direct current motor cortex stimulation in mice
Zheng Gan, Han Li, Paul Vincent Naser, Manfred Josef Oswald, Rohini Kuner · 2021 · Scientific Reports
CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping
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3D imaging for driving cancer discovery
Ravian L. van Ineveld, Esmée J. van Vliet, Ellen J. Wehrens, María Alieva, Anne C. Rios · 2022 · The EMBO Journal
Atlas of exercise-induced brain activation in mice
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Loss of CXCR4/CXCL12 Signaling Causes Oculomotor Nerve Misrouting and Development of Motor Trigeminal to Oculomotor Synkinesis
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Fast, 3D Isotropic Imaging of Whole Mouse Brain Using Multiangle‐Resolved Subvoxel SPIM
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METTL3 Is Involved in the Development of Graves’ Disease by Inducing SOCS mRNA m6A Modification
Ronghua Song, Peng Du, Chaoqun Gao, Xuerong Liu, Jin‐an Zhang · 2021 · Frontiers in Endocrinology
Characteristic Features of Deep Brain Lymphatic Vessels and Their Regulation by Chronic Stress
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TAAR1 agonists improve glycemic control, reduce body weight and modulate neurocircuits governing energy balance and feeding
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Photoacoustic Tomography with Temporal Encoding Reconstruction (PATTERN) for cross-modal individual analysis of the whole brain
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Neurons for infant social behaviors in the mouse zona incerta
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Distinct dynamics and intrinsic properties in ventral tegmental area populations mediate reward association and motivation
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Astrid Tjitske van der Geest, Channa E Jakobs, Tijana Ljubikj, Christiaan F. M. Huffels, Marta Cañizares Luna, Renata Vieira de Sá, Youri Adolfs, Marina de Wit, Daan H. Rutten, Marthe Kaal et al. · 2024 · Acta Neuropathologica Communications
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