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Ye Z, Shelton AM, Shaker JR, Boussard J, Colonell J, Birman D, Manavi S, Chen S, Windolf C, Hurwitz C, Namima T, Pedraja F, Weiss S, Raducanu B, Ness TV, Jia X, Mastroberardino G, Rossi LF, Carandini M, Häusser M, Einevoll GT, Laurent G, Sawtell NB, Bair W, Pasupathy A, Lopez CM, Dutta B, Paninski L, Siegle JH, Koch C, Olsen SR, Harris TD, Steinmetz NA. Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings. bioRxiv 2024:2023.08.23.554527. [PMID: 37662298 PMCID: PMC10473688 DOI: 10.1101/2023.08.23.554527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device samples neuronal activity at ultra-high spatial density (~10 times higher than previous probes) with low noise levels, while trading off recording span. NP Ultra is effectively an implantable voltage-sensing camera that captures a planar image of a neuron's electrical field. We use a spike sorting algorithm optimized for these probes to demonstrate that the yield of visually-responsive neurons in recordings from mouse visual cortex improves up to ~3-fold. We show that NP Ultra can record from small neuronal structures including axons and dendrites. Recordings across multiple brain regions and four species revealed a subset of extracellular action potentials with unexpectedly small spatial spread and axon-like features. We share a large-scale dataset of these brain-wide recordings in mice as a resource for studies of neuronal biophysics. Finally, using ground-truth identification of three major inhibitory cortical cell types, we found that these cell types were discriminable with approximately 75% success, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, detection of subcellular compartments, and cell type classification to enable more powerful dissection of neural circuit activity during behavior.
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Affiliation(s)
- Zhiwen Ye
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Andrew M. Shelton
- MindScope Program, Allen Institute, Seattle, WA, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Jordan R. Shaker
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Julien Boussard
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Daniel Birman
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Sahar Manavi
- MindScope Program, Allen Institute, Seattle, WA, USA
| | - Susu Chen
- Janelia Research Campus, Ashburn, VA, USA
| | - Charlie Windolf
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Cole Hurwitz
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Tomoyuki Namima
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, Seattle, WA, USA
| | - Federico Pedraja
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Shahaf Weiss
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | | | | | - Xiaoxuan Jia
- Center for Life Sciences & IDG/McGovern Institute for Brain Research, Tsinghua University, China
| | - Giulia Mastroberardino
- UCL Institute of Ophthalmology, University College London, London, UK
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - L. Federico Rossi
- Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Matteo Carandini
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Michael Häusser
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Gaute T. Einevoll
- Norwegian University of Life Sciences, Ås, Norway
- University of Oslo, Oslo, Norway
| | - Gilles Laurent
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Nathaniel B. Sawtell
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Wyeth Bair
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, Seattle, WA, USA
| | - Anitha Pasupathy
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, Seattle, WA, USA
| | | | | | - Liam Paninski
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Christof Koch
- MindScope Program, Allen Institute, Seattle, WA, USA
| | - Shawn R. Olsen
- MindScope Program, Allen Institute, Seattle, WA, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Timothy D. Harris
- Janelia Research Campus, Ashburn, VA, USA
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD, USA
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Birman D, Fox KJ, Gardner JL. Poster Session I: Gain, not changes in spatial receptive field properties, improves task performance in a neural network attention model. J Vis 2023; 23:26. [PMID: 38109622 DOI: 10.1167/jov.23.15.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
Attention allows us to focus sensory processing on behaviorally relevant aspects of the visual world. One potential mechanism of attention is a change in the gain of sensory responses. However, changing gain at early stages could have multiple downstream consequences for visual processing. Which, if any, of these effects can account for the benefits of attention for detection and discrimination? Using a model of primate visual cortex we document how a Gaussian-shaped gain modulation results in changes to spatial tuning properties. Forcing the model to use only these changes failed to produce any benefit in task performance. Instead, we found that gain alone was both necessary and sufficient to explain category detection and discrimination during attention. Our results show how gain can give rise to changes in receptive fields which are not necessary for enhancing task performance.
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Affiliation(s)
- Daniel Birman
- Department of Biological Structure, University of Washington
| | - Kai J Fox
- Department of Psychology, Stanford University
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Birman D, Yang KJ, West SJ, Karsh B, Browning Y, Siegle JH, Steinmetz NA. Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment. bioRxiv 2023:2023.07.14.548952. [PMID: 37503284 PMCID: PMC10369935 DOI: 10.1101/2023.07.14.548952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Targeting deep brain structures during electrophysiology and injections requires intensive training and expertise. Even with experience, researchers often can't be certain that a probe is placed precisely in a target location and this complexity scales with the number of simultaneous probes used in an experiment. Here, we present Pinpoint, open-source software that allows for interactive exploration of stereotaxic insertion plans. Once an insertion plan is created, Pinpoint allows users to save these online and share them with collaborators. 3D modeling tools allow users to explore their insertions alongside rig and implant hardware and ensure plans are physically possible. Probes in Pinpoint can be linked to electronic micro-manipulators allowing real-time visualization of current brain region targets alongside neural data. In addition, Pinpoint can control manipulators to automate and parallelize the insertion process. Compared to previously available software, Pinpoint's easy access through web browsers, extensive features, and real-time experiment integration enable more efficient and reproducible recordings.
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Affiliation(s)
- Daniel Birman
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Kenneth J. Yang
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Steven J. West
- Sainsbury Wellcome Centre, London W1T 4JG, United Kingdom
| | - Bill Karsh
- HHMI Janelia Research Campus, Ashburn, Virginia 20147, USA
| | - Yoni Browning
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | | | | | - Nicholas A. Steinmetz
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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Fox KJ, Birman D, Gardner JL. Gain, not concomitant changes in spatial receptive field properties, improves task performance in a neural network attention model. eLife 2023; 12:78392. [PMID: 37184221 DOI: 10.7554/elife.78392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/12/2023] [Indexed: 05/16/2023] Open
Abstract
Attention allows us to focus sensory processing on behaviorally relevant aspects of the visual world. One potential mechanism of attention is a change in the gain of sensory responses. However, changing gain at early stages could have multiple downstream consequences for visual processing. Which, if any, of these effects can account for the benefits of attention for detection and discrimination? Using a model of primate visual cortex we document how a Gaussian-shaped gain modulation results in changes to spatial tuning properties. Forcing the model to use only these changes failed to produce any benefit in task performance. Instead, we found that gain alone was both necessary and sufficient to explain category detection and discrimination during attention. Our results show how gain can give rise to changes in receptive fields which are not necessary for enhancing task performance.
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Affiliation(s)
- Kai J Fox
- Department of Psychology, Stanford University, Stanford, United States
| | - Daniel Birman
- Department of Biological Structure, University of Washington, Seattle, United States
| | - Justin L Gardner
- Department of Psychology, Stanford University, Stanford, United States
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Birman D, Gardner JL. Putting spatial and feature-based attention on a shared perceptual metric. J Vis 2019. [DOI: 10.1167/19.10.269a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Abstract
Attention can both enhance and suppress cortical sensory representations. However, changing sensory representations can also be detrimental to behavior. Behavioral consequences can be avoided by flexibly changing sensory readout, while leaving the representations unchanged. Here, we asked human observers to attend to and report about either one of two features which control the visibility of motion while making concurrent measurements of cortical activity with BOLD imaging (fMRI). We extend a well-established linking model to account for the relationship between these measurements and find that changes in sensory representation during directed attention are insufficient to explain perceptual reports. Adding a flexible downstream readout is necessary to best explain our data. Such a model implies that observers should be able to recover information about ignored features, a prediction which we confirm behaviorally. Thus, flexible readout is a critical component of the cortical implementation of human adaptive behavior.
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Affiliation(s)
- Daniel Birman
- Department of Psychology, Stanford University, Stanford, CA, 94305, USA.
| | - Justin L Gardner
- Department of Psychology, Stanford University, Stanford, CA, 94305, USA
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Abstract
Despite the central use of motion visibility to reveal the neural basis of perception, perceptual decision making, and sensory inference there exists no comprehensive quantitative framework establishing how motion visibility parameters modulate human cortical response. Random-dot motion stimuli can be made less visible by reducing image contrast or motion coherence, or by shortening the stimulus duration. Because each of these manipulations modulates the strength of sensory neural responses they have all been extensively used to reveal cognitive and other nonsensory phenomena such as the influence of priors, attention, and choice-history biases. However, each of these manipulations is thought to influence response in different ways across different cortical regions and a comprehensive study is required to interpret this literature. Here, human participants observed random-dot stimuli varying across a large range of contrast, coherence, and stimulus durations as we measured blood-oxygen-level dependent responses. We developed a framework for modeling these responses that quantifies their functional form and sensitivity across areas. Our framework demonstrates the sensitivity of all visual areas to each parameter, with early visual areas V1-V4 showing more parametric sensitivity to changes in contrast and V3A and the human middle temporal area to coherence. Our results suggest that while motion contrast, coherence, and duration share cortical representation, they are encoded with distinct functional forms and sensitivity. Thus, our quantitative framework serves as a reference for interpretation of the vast perceptual literature manipulating these parameters and shows that different manipulations of visibility will have different effects across human visual cortex and need to be interpreted accordingly. NEW & NOTEWORTHY Manipulations of motion visibility have served as a key tool for understanding the neural basis for visual perception. Here we measured human cortical response to changes in visibility across a comprehensive range of motion visibility parameters and modeled these with a quantitative framework. Our quantitative framework can be used as a reference for linking human cortical response to perception and underscores that different manipulations of motion visibility can have greatly different effects on cortical representation.
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Affiliation(s)
- Daniel Birman
- Department of Psychology, Stanford University , Stanford, California
| | - Justin L Gardner
- Department of Psychology, Stanford University , Stanford, California
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Esteban O, Birman D, Schaer M, Koyejo OO, Poldrack RA, Gorgolewski KJ. MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites. PLoS One 2017; 12:e0184661. [PMID: 28945803 PMCID: PMC5612458 DOI: 10.1371/journal.pone.0184661] [Citation(s) in RCA: 402] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 08/28/2017] [Indexed: 12/22/2022] Open
Abstract
Quality control of MRI is essential for excluding problematic acquisitions and avoiding bias in subsequent image processing and analysis. Visual inspection is subjective and impractical for large scale datasets. Although automated quality assessments have been demonstrated on single-site datasets, it is unclear that solutions can generalize to unseen data acquired at new sites. Here, we introduce the MRI Quality Control tool (MRIQC), a tool for extracting quality measures and fitting a binary (accept/exclude) classifier. Our tool can be run both locally and as a free online service via the OpenNeuro.org portal. The classifier is trained on a publicly available, multi-site dataset (17 sites, N = 1102). We perform model selection evaluating different normalization and feature exclusion approaches aimed at maximizing across-site generalization and estimate an accuracy of 76%±13% on new sites, using leave-one-site-out cross-validation. We confirm that result on a held-out dataset (2 sites, N = 265) also obtaining a 76% accuracy. Even though the performance of the trained classifier is statistically above chance, we show that it is susceptible to site effects and unable to account for artifacts specific to new sites. MRIQC performs with high accuracy in intra-site prediction, but performance on unseen sites leaves space for improvement which might require more labeled data and new approaches to the between-site variability. Overcoming these limitations is crucial for a more objective quality assessment of neuroimaging data, and to enable the analysis of extremely large and multi-site samples.
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Affiliation(s)
- Oscar Esteban
- Department of Psychology, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Daniel Birman
- Department of Psychology, Stanford University, Stanford, California, United States of America
| | - Marie Schaer
- Department of Psychiatry, University of Geneva School of Medicine, Geneva, Switzerland
| | - Oluwasanmi O. Koyejo
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, United States of America
| | - Russell A. Poldrack
- Department of Psychology, Stanford University, Stanford, California, United States of America
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Affiliation(s)
- Daniel Birman
- Department of Psychology, Stanford University, Stanford, California, USA
| | - Justin L Gardner
- Department of Psychology, Stanford University, Stanford, California, USA
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Schultze-Kraft M, Birman D, Rusconi M, Allefeld C, Görgen K, Dähne S, Blankertz B, Haynes JD. The point of no return in vetoing self-initiated movements. Proc Natl Acad Sci U S A 2016; 113:1080-5. [PMID: 26668390 PMCID: PMC4743787 DOI: 10.1073/pnas.1513569112] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In humans, spontaneous movements are often preceded by early brain signals. One such signal is the readiness potential (RP) that gradually arises within the last second preceding a movement. An important question is whether people are able to cancel movements after the elicitation of such RPs, and if so until which point in time. Here, subjects played a game where they tried to press a button to earn points in a challenge with a brain-computer interface (BCI) that had been trained to detect their RPs in real time and to emit stop signals. Our data suggest that subjects can still veto a movement even after the onset of the RP. Cancellation of movements was possible if stop signals occurred earlier than 200 ms before movement onset, thus constituting a point of no return.
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Affiliation(s)
- Matthias Schultze-Kraft
- Bernstein Center for Computational Neuroscience, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Neurotechnology Group, Technische Universität Berlin, 10587 Berlin, Germany; Bernstein Focus: Neurotechnology, Technische Universität Berlin, 10587 Berlin, Germany;
| | - Daniel Birman
- Bernstein Center for Computational Neuroscience, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Berlin Center for Advanced Neuroimaging, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Marco Rusconi
- Bernstein Center for Computational Neuroscience, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Berlin Center for Advanced Neuroimaging, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Carsten Allefeld
- Bernstein Center for Computational Neuroscience, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Berlin Center for Advanced Neuroimaging, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Kai Görgen
- Bernstein Center for Computational Neuroscience, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Berlin Center for Advanced Neuroimaging, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Sven Dähne
- Machine Leaning Group, Technische Universität Berlin, 10587 Berlin, Germany
| | - Benjamin Blankertz
- Bernstein Center for Computational Neuroscience, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Neurotechnology Group, Technische Universität Berlin, 10587 Berlin, Germany; Bernstein Focus: Neurotechnology, Technische Universität Berlin, 10587 Berlin, Germany
| | - John-Dylan Haynes
- Bernstein Center for Computational Neuroscience, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Bernstein Focus: Neurotechnology, Technische Universität Berlin, 10587 Berlin, Germany; Berlin Center for Advanced Neuroimaging, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Cluster of Excellence NeuroCure, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Department of Psychology, Humboldt Universität zu Berlin, 12489 Berlin, Germany; Clinic of Neurology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
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Abstract
The present study investigated acculturation to the Hispanic and American cultures and self-perceptions of competence among 123 Latino immigrant adolescents. The study tested a contextual model of biculturalism by examining whether different acculturation styles predicted perceived competence in life spheres with different cultural demands. Perceived competence was assessed using Harter's (1988). Self-Perceptions of Competence Profile for Adolescents for the life spheres of school, peers (both Latino and non-Latino), and global self-worth. In addition, an analogous scale to assess perceptions of competence in the family was constructed for that sphere. The study found some support for a contextual model of acculturation. Acculturation to American culture predicted positive self-perceptions of competence with American peers, while acculturation to Hispanic culture predicted positive self-perceptions of competence with Latino peers. Perceived family competence, however, was predicted by acculturation to American rather than Hispanic culture. Results with respect to biculturalism are tentative, with a trend relating biculturalism to positive self-perceptions of global self-worth. However, because many of the conditions stipulated by the model were not met, results with respect to biculturalism raise questions about current approaches to operationalizing the construct.
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Affiliation(s)
- D Birman
- National Institute of Mental Health, USA
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Birman D, Tyler FB. Acculturation and alienation of Soviet Jewish refugees in the United States. Genet Soc Gen Psychol Monogr 1994; 120:101-115. [PMID: 8174934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We examined the relationship of identity and behavioral acculturation to alienation among 49 Soviet Jewish refugees in the United States in 1987. For all the subjects, acculturation was best described as a unilevel rather than a bilevel or multilevel process, because a negative relationship was found between acculturation and the American and Russian cultures. For women, finding an American identity was related to length of residence, whereas holding on to a Russian identity as well as behavioral acculturation predicted alienation. For men, however, a multicultural process appeared to exist with respect to behavioral acculturation, although holding on to a Russian identity was positively related to alienation. Thus, men were able to continue to participate in Russian-oriented activities without feeling alienated, and this participation appeared to increase with length of residence in the United States.
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Affiliation(s)
- D Birman
- Refugee Mental Health Branch, Substance Abuse and Mental Health Services Administration, Rockville, MD 20857
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