scitex 2.17.0__py3-none-any.whl → 2.17.3__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (73) hide show
  1. scitex/_dev/__init__.py +122 -0
  2. scitex/_dev/_config.py +391 -0
  3. scitex/_dev/_dashboard/__init__.py +11 -0
  4. scitex/_dev/_dashboard/_app.py +89 -0
  5. scitex/_dev/_dashboard/_routes.py +169 -0
  6. scitex/_dev/_dashboard/_scripts.py +301 -0
  7. scitex/_dev/_dashboard/_styles.py +205 -0
  8. scitex/_dev/_dashboard/_templates.py +117 -0
  9. scitex/_dev/_dashboard/static/version-dashboard-favicon.svg +12 -0
  10. scitex/_dev/_ecosystem.py +109 -0
  11. scitex/_dev/_github.py +360 -0
  12. scitex/_dev/_mcp/__init__.py +11 -0
  13. scitex/_dev/_mcp/handlers.py +182 -0
  14. scitex/_dev/_ssh.py +332 -0
  15. scitex/_dev/_versions.py +272 -0
  16. scitex/_mcp_tools/__init__.py +2 -0
  17. scitex/_mcp_tools/dev.py +186 -0
  18. scitex/audio/_audio_check.py +84 -41
  19. scitex/cli/capture.py +45 -22
  20. scitex/cli/dev.py +494 -0
  21. scitex/cli/main.py +2 -0
  22. scitex/cli/stats.py +48 -20
  23. scitex/cli/verify.py +33 -36
  24. scitex/plt/__init__.py +16 -6
  25. scitex/scholar/url_finder/.tmp/open_url/KNOWN_RESOLVERS.py +462 -0
  26. scitex/scholar/url_finder/.tmp/open_url/README.md +223 -0
  27. scitex/scholar/url_finder/.tmp/open_url/_DOIToURLResolver.py +694 -0
  28. scitex/scholar/url_finder/.tmp/open_url/_OpenURLResolver.py +1160 -0
  29. scitex/scholar/url_finder/.tmp/open_url/_ResolverLinkFinder.py +344 -0
  30. scitex/scholar/url_finder/.tmp/open_url/__init__.py +24 -0
  31. scitex/template/__init__.py +18 -1
  32. scitex/template/clone_research_minimal.py +111 -0
  33. scitex/verify/README.md +0 -12
  34. scitex/verify/__init__.py +0 -4
  35. scitex/verify/_visualize.py +0 -4
  36. scitex/verify/_viz/__init__.py +0 -18
  37. {scitex-2.17.0.dist-info → scitex-2.17.3.dist-info}/METADATA +2 -1
  38. {scitex-2.17.0.dist-info → scitex-2.17.3.dist-info}/RECORD +41 -49
  39. scitex/dev/plt/data/mpl/PLOTTING_FUNCTIONS.yaml +0 -90
  40. scitex/dev/plt/data/mpl/PLOTTING_SIGNATURES.yaml +0 -1571
  41. scitex/dev/plt/data/mpl/PLOTTING_SIGNATURES_DETAILED.yaml +0 -6262
  42. scitex/dev/plt/data/mpl/SIGNATURES_FLATTENED.yaml +0 -1274
  43. scitex/dev/plt/data/mpl/dir_ax.txt +0 -459
  44. scitex/scholar/data/.gitkeep +0 -0
  45. scitex/scholar/data/README.md +0 -44
  46. scitex/scholar/data/bib_files/bibliography.bib +0 -1952
  47. scitex/scholar/data/bib_files/neurovista.bib +0 -277
  48. scitex/scholar/data/bib_files/neurovista_enriched.bib +0 -441
  49. scitex/scholar/data/bib_files/neurovista_enriched_enriched.bib +0 -441
  50. scitex/scholar/data/bib_files/neurovista_processed.bib +0 -338
  51. scitex/scholar/data/bib_files/openaccess.bib +0 -89
  52. scitex/scholar/data/bib_files/pac-seizure_prediction_enriched.bib +0 -2178
  53. scitex/scholar/data/bib_files/pac.bib +0 -698
  54. scitex/scholar/data/bib_files/pac_enriched.bib +0 -1061
  55. scitex/scholar/data/bib_files/pac_processed.bib +0 -0
  56. scitex/scholar/data/bib_files/pac_titles.txt +0 -75
  57. scitex/scholar/data/bib_files/paywalled.bib +0 -98
  58. scitex/scholar/data/bib_files/related-papers-by-coauthors.bib +0 -58
  59. scitex/scholar/data/bib_files/related-papers-by-coauthors_enriched.bib +0 -87
  60. scitex/scholar/data/bib_files/seizure_prediction.bib +0 -694
  61. scitex/scholar/data/bib_files/seizure_prediction_processed.bib +0 -0
  62. scitex/scholar/data/bib_files/test_complete_enriched.bib +0 -437
  63. scitex/scholar/data/bib_files/test_final_enriched.bib +0 -437
  64. scitex/scholar/data/bib_files/test_seizure.bib +0 -46
  65. scitex/scholar/data/impact_factor/JCR_IF_2022.xlsx +0 -0
  66. scitex/scholar/data/impact_factor/JCR_IF_2024.db +0 -0
  67. scitex/scholar/data/impact_factor/JCR_IF_2024.xlsx +0 -0
  68. scitex/scholar/data/impact_factor/JCR_IF_2024_v01.db +0 -0
  69. scitex/scholar/data/impact_factor.db +0 -0
  70. scitex/verify/_viz/_plotly.py +0 -193
  71. {scitex-2.17.0.dist-info → scitex-2.17.3.dist-info}/WHEEL +0 -0
  72. {scitex-2.17.0.dist-info → scitex-2.17.3.dist-info}/entry_points.txt +0 -0
  73. {scitex-2.17.0.dist-info → scitex-2.17.3.dist-info}/licenses/LICENSE +0 -0
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- title={Quantification of Phase-Amplitude Coupling in Neuronal Oscillations: Comparison of Phase-Locking Value, Mean Vector Length, Modulation Index, and Generalized-Linear-Modeling-Cross-Frequency-Coupling},
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- journal={Frontiers in Neuroscience},
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- year={2019},
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- volume={13},
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- @article{Friston2020GenerativeMLB,
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- volume={118},
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- pages={42 - 64},
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- url={https://api.semanticscholar.org/CorpusId:220603864}
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- }
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-
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- @article{Canolty2010TheFRC,
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- title={The functional role of cross-frequency coupling},
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- author={R. Canolty and R. Knight},
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- journal={Trends in Cognitive Sciences},
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- volume={14},
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- pages={506-515},
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- url={https://www.sciencedirect.com/science/article/pii/S1364661310002068?dgcid=api\_sd\_search-api-endpoint}
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- }
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-
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- @article{Aru2014UntanglingCCD,
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- title={Untangling cross-frequency coupling in neuroscience},
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- journal={Current Opinion in Neurobiology},
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- year={2014},
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- volume={31},
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- pages={51-61},
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- url={https://www.sciencedirect.com/science/article/pii/S0959438814001640?dgcid=api\_sd\_search-api-endpoint}
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- }
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- @article{Tort2010MeasuringPCE,
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- journal={Journal of neurophysiology},
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- }
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-
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- @inproceedings{PintoOrellana2023StatisticalIFF,
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- title={Statistical Inference for Modulation Index in Phase-Amplitude Coupling},
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- author={Marco Pinto-Orellana and H. Ombao and Beth A. Lopour},
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- year={2023},
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- url={https://api.semanticscholar.org/CorpusId:263829747}
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- }
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-
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- @article{Wodeyar2023DifferentMTG,
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- title={Different Methods to Estimate the Phase of Neural Rhythms Agree But Only During Times of Low Uncertainty},
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- author={Anirudh Wodeyar and François A Marshall and C. Chu and Uri T. Eden and Mark A. Kramer},
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- journal={eNeuro},
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- year={2023},
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- volume={10},
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- url={https://api.semanticscholar.org/CorpusId:264098986}
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- }
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-
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- @article{Formoso2021ModellingBCH,
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- title={Modelling Brain Connectivity Networks by Graph Embedding for Dyslexia Diagnosis},
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- author={M. Formoso and A. Ortiz and F. J. Mart'inez-Murcia and N. Gallego-Molina and J. Luque},
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- journal={ArXiv},
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- year={2021},
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- volume={abs/2104.05497},
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- url={https://api.semanticscholar.org/CorpusId:233209974}
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- }
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-
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- @article{Yin2021EstimatingPAI,
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- title={Estimating Phase Amplitude Coupling between Neural Oscillations Based on Permutation and Entropy},
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- author={Liyong Yin and Fan Tian and R. Hu and Zhaohui Li and F. Yin},
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- journal={Entropy},
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- year={2021},
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- volume={23},
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- url={https://api.semanticscholar.org/CorpusId:237322109}
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- }
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-
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- @article{Dvok2014TowardAPJ,
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- title={Toward a proper estimation of phase–amplitude coupling in neural oscillations},
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- author={Dino Dvoř{\'a}k and A. Fenton},
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- }
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-
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- @article{Munia2019TimeFrequencyBPK,
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- title={Time-Frequency Based Phase-Amplitude Coupling Measure For Neuronal Oscillations},
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- author={T. T. Munia and Selin Aviyente},
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- journal={Scientific Reports},
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- year={2019},
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- volume={9},
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- url={https://api.semanticscholar.org/CorpusId:201651743}
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- }
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- @article{Sheng2024EffectOPL,
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- title={Effect of Phase Clustering Bias on Phase-Amplitude Coupling for Emotional EEG.},
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- author={Tingyu Sheng and Qiansheng Feng and Zhiguo Luo and Shaokai Zhao and Minpeng Xu and Dong Ming and Ye Yan and Erwei Yin},
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- journal={Journal of integrative neuroscience},
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- year={2024},
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- volume={23 2},
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- pages={
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- 33
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- },
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- url={https://api.semanticscholar.org/CorpusId:267970715}
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- }
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-
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- @article{Scherer2022DirectMIM,
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- title={Direct modulation index: A measure of phase amplitude coupling for neurophysiology data},
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- author={Maximilian Scherer and Tianlu Wang and R. Guggenberger and L. Milosevic and A. Gharabaghi},
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- journal={Human Brain Mapping},
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- year={2022},
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- volume={44},
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- pages={1862 - 1867},
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- url={https://doi.org/10.1002/hbm.26190}
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- }
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-
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- @article{Bergmann2018PhaseAmplitudeCAN,
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- title={Phase-Amplitude Coupling: A General Mechanism for Memory Processing and Synaptic Plasticity?},
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- author={T. Bergmann and J. Born},
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- journal={Neuron},
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- year={2018},
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- volume={97},
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- url={https://www.sciencedirect.com/science/article/pii/S0896627317311704?dgcid=api\_sd\_search-api-endpoint}
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- }
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- @article{Cox2020AnalyzingHSO,
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- title={Analyzing human sleep EEG: A methodological primer with code implementation.},
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- author={Roy Cox and J. Fell},
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- journal={Sleep medicine reviews},
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- year={2020},
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- volume={54},
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- pages={
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- 101353
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- },
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- url={https://api.semanticscholar.org/CorpusId:220907907}
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- }
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-
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- @article{Gwon2021AlphaAHP,
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- title={Alpha and high gamma phase amplitude coupling during motor imagery and weighted cross-frequency coupling to extract discriminative cross-frequency patterns},
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- author={Dae-Cheol Gwon and M. Ahn},
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- journal={NeuroImage},
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- year={2021},
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- volume={240},
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- url={https://api.semanticscholar.org/CorpusId:235917686}
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- }
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- @article{Rakowska2021LongTEQ,
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- title={Long term effects of cueing procedural memory reactivation during NREM sleep},
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- journal={Neuroimage},
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- year={2021},
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- volume={244},
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- url={https://api.semanticscholar.org/CorpusId:237541152}
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- @article{Jensen2016DiscriminatingVFR,
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- volume={3},
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- url={https://api.semanticscholar.org/CorpusId:9897413}
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- @article{Ebrahimvand2025CrossFrequencyCRS,
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- title={Cross‐Frequency Couplings Reveal Mice Visual Cortex Selectivity to Grating Orientations},
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- year={2025},
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- volume={15},
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- @article{Ahn2022TheFIT,
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- title={The Functional Interactions between Cortical Regions through Theta-Gamma Coupling during Resting-State and a Visual Working Memory Task},
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- author={Ji-Seon Ahn and Jaeseok Heo and Jooyoung Oh and Deokjong Lee and K. Jhung and Jae-Jin Kim and Jin Young Park},
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- journal={Brain Sciences},
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- @article{GallegoMolina2021ComplexNMU,
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- title={Complex network modelling of EEG band coupling in dyslexia: An exploratory analysis of auditory processing and diagnosis},
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- journal={Knowledge-Based Systems},
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- @article{Voytek2010ShiftsIGV,
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- @article{Seymour2017TheDOX,
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- title={The Detection of Phase Amplitude Coupling during Sensory Processing},
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- author={Robert A. Seymour and Gina Rippon and Klaus Kessler},
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- journal={Frontiers in Neuroscience},
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- year={2017},
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- volume={11},
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- url={https://api.semanticscholar.org/CorpusId:19922713}
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- }
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-
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- @article{Li2021MeasuringPCY,
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- title={Measuring Phase-Amplitude Coupling Based on the Jensen-Shannon Divergence and Correlation Matrix},
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- author={Zhaohui Li and Xiaochen Bai and R. Hu and Xiaoli Li},
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- journal={IEEE Transactions on Neural Systems and Rehabilitation Engineering},
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- year={2021},
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- url={https://api.semanticscholar.org/CorpusId:235776537}
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- }
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- @article{Cohen2009OscillatoryAAZ,
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- @article{Cox2019HeterogeneousPOAA,
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- title={Heterogeneous profiles of coupled sleep oscillations in human hippocampus},
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- author={Roy Cox and Theodor R{\"u}ber and B. Staresina and J. Fell},
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- journal={Neuroimage},
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- year={2019},
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- volume={202},
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- url={https://api.semanticscholar.org/CorpusId:109858184}
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- }
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-
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- @article{Munia2021MultivariateAOAB,
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- title={Multivariate Analysis of Bivariate Phase-Amplitude Coupling in EEG Data Using Tensor Robust PCA},
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- author={T. T. Munia and Selin Aviyente},
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- journal={IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society},
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- year={2021},
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- volume={29},
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- pages={1268 - 1279},
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- url={https://api.semanticscholar.org/CorpusId:235675330}
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- }
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-
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- @article{Meij2012PhaseAmplitudeCIAC,
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- title={Phase–Amplitude Coupling in Human Electrocorticography Is Spatially Distributed and Phase Diverse},
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- @article{RojasLbano2014TheOBAD,
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- journal={Frontiers in Behavioral Neuroscience},
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- year={2014},
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- volume={8},
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- url={https://api.semanticscholar.org/CorpusId:17638335}
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- }
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-
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- @article{Mikutta2019PhaseamplitudeCOAE,
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- title={Phase‐amplitude coupling of sleep slow oscillatory and spindle activity correlates with overnight memory consolidation},
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- author={C. Mikutta and B. Feige and J. Maier and E. Hertenstein and J. Holz and D. Riemann and C. Nissen},
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- journal={Journal of Sleep Research},
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- year={2019},
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- volume={28},
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- url={https://doi.org/10.1111/jsr.12835}
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- }
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-
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- @article{GarcaRosales2020PhaseamplitudeCPAF,
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- title={Phase-amplitude coupling profiles differ in frontal and auditory cortices},
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- author={Francisco Garc{\'i}a-Rosales and Luciana L{\'o}pez-Jury and Eugenia Gonz{\'a}lez-Palomares and Yuranny Cabral-Calder{\'i}n and M. K{\"o}ssl and Julio C. Hechavarr{\'i}a},
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- journal={bioRxiv},
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- year={2020},
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- url={https://api.semanticscholar.org/CorpusId:218571850}
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- }
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-
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- @article{Zhang2017TemporalspatialCOAG,
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- title={Temporal-spatial characteristics of phase-amplitude coupling in electrocorticogram for human temporal lobe epilepsy},
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- author={Ruihua Zhang and Ye Ren and Chunyan Liu and Na Xu and Xiaoli Li and F. Cong and T. Ristaniemi and Yuping Wang},
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- journal={Clinical Neurophysiology},
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- year={2017},
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- volume={128},
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- url={https://www.sciencedirect.com/science/article/pii/S138824571730216X?dgcid=api\_sd\_search-api-endpoint}
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- }
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-
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- @article{Combrisson2020TensorpacAOAH,
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- title={Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals},
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- author={Etienne Combrisson and T. Nest and A. Brovelli and Robin A. A. Ince and Juan L. P. Soto and A. Guillot and K. Jerbi},
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- journal={PLoS Computational Biology},
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- year={2020},
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- volume={16},
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- url={https://www.ncbi.nlm.nih.gov/pubmed/33119593}
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- }
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-
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- @article{Onslow2014ACCAI,
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- title={A Canonical Circuit for Generating Phase-Amplitude Coupling},
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- author={Angela C. E. Onslow and Matthew W. Jones and R. Bogacz},
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- journal={PLoS ONE},
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- year={2014},
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- volume={9},
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- url={https://api.semanticscholar.org/CorpusId:157901}
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- }
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-
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- @article{Kesebir2019CFCDIAJ,
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- title={CFC delta-beta is related with mixed features and response to treatment in bipolar II depression},
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- author={S. Kesebir and R. M. Demirer and N. Tarhan},
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- journal={Heliyon},
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- year={2019},
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- volume={5},
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- url={https://api.semanticscholar.org/CorpusId:196556378}
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- }
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-
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- @article{Ohki2019TimingOPAK,
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- title={Timing of phase‐amplitude coupling is essential for neuronal and functional maturation of audiovisual integration in adolescents},
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- author={Takefumi Ohki and T. Matsuda and A. Gunji and Y. Takei and Ryusuke Sakuma and Y. Kaneko and M. Inagaki and T. Hanakawa and Kazuhiro Ueda and M. Fukuda and K. Hiraki},
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- journal={Brain and Behavior},
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- year={2019},
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- volume={10},
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- url={https://api.semanticscholar.org/CorpusId:216596437}
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- }
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-
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- @article{FitzGerald2013CrossfrequencyCWAL,
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- title={Cross-frequency coupling within and between the human thalamus and neocortex},
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- author={Thomas H. B. FitzGerald and A. Valent{\'i}n and R. Selway and M. Richardson},
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- journal={Frontiers in Human Neuroscience},
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- year={2013},
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