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{ "kind": "infographic", "prompt": "Canonical biophysical astrocyte Ca²⁺ oscillation models — quantitative parameters and experimental disagreement", "provider": "other", "raw_fields": { "title": "Canonical biophysical astrocyte Ca²⁺ oscillation models — quantitative parameters and experimental disagreement", "data_points": [ { "doi": "10.3389/fncel.2025.1536096", "study": "Musotto et al. 2025", "value": "stable-amplitude, fairly constant-frequency oscillations throughout 87 s — no activation → peak → decline envelope", "method": "Numerical ODE integration with the originally published parameters (VM2, VM3, Hill coefficients n, m, p; threshold constants K2, KR, KA) extended from 10 s to 87 s", "metric": "oscillation regularity over 87 s", "study_system": "Goldbeter 1990 minimal-CICR model re-integrated over the experimental observation window (87 s)", "value_source_section": "The Goldbeter model", "value_source_sentence": "By extending the integration time of the model to 87 s, so as to be comparable with the experimental time, it can be observed that the Z oscillations persist throughout the interval with a fairly stable amplitude and frequency." }, { "doi": "10.3389/fncom.2018.00014", "study": "Manninen et al. 2018 (Computational Models for Calcium-Mediated Astrocyte Functions)", "value": "the De Young–Keizer (1992) and Li-Rinzel (1994) IP3R gating schemes (or modifications) are the dominant backbones used across astrocyte Ca²⁺ models", "method": "Classification of ~100 astrocyte Ca²⁺ models by core IP3R dynamics and parameterisation lineage", "metric": "prevalence of De Young–Keizer / Li-Rinzel backbone across the field", "study_system": "Field-wide review of astrocyte Ca²⁺ models in ≈100 biophysical publications", "value_source_section": "2.3. Characteristics of models", "value_source_sentence": "Most of the astrocyte models utilized the Ca2+ dynamics models by De Young and Keizer (1992) and Li and Rinzel (1994), or a modification of them, even though these two models were not made to describe astrocytic behavior (Manninen et al., 2018)." }, { "doi": "10.1155/2016/7607924", "study": "De Pittà & Brunel 2016 – Li-Rinzel CICR adoption and gliotransmission threshold", "value": "C_θ ≈ 0.15–0.8 μM cytosolic Ca²⁺", "method": "Hodgkin–Huxley-style IP3R gating equations per Li & Rinzel 1994; glutamate exocytosis threshold tuned to published astrocyte experiments", "metric": "astrocytic Ca²⁺ threshold for glutamate exocytosis (C_θ)", "study_system": "Tripartite synapse model with Li-Rinzel CICR driving Ca²⁺-dependent astrocytic glutamate exocytosis", "value_source_section": "B.3. Gliotransmission", "value_source_sentence": "Exocytosis of glutamate from astrocytes is reported to occur by Ca2+ concentrations increasing beyond a threshold value C θ ≈ 0.15–0.8 μM." }, { "doi": "10.3389/fncom.2014.00045", "study": "Lallouette et al. 2014 – ChI Ca²⁺-IP3 model in 3-D networks", "value": "< 0.1 μM·s⁻¹ → ICW propagation blocked (IP3 diffusion slower than degradation)", "method": "Gap-junction-coupled point-like astrocytes; inter-cellular IP3 flux J_diff with threshold gradient I_θ; coupling strength F swept", "metric": "IP3 diffusion-flux floor below which intercellular calcium waves (ICW) are blocked", "study_system": "3-D astrocyte network using the Ca²⁺-IP3 (ChI) model of De Pittà 2009 with variables (C, h, I) and gap-junction IP3 diffusion", "value_source_section": "The influence of the coupling strength is non–monotonic", "value_source_sentence": "For very low values of F (〈ΣF〉 < 0.1 μM.s−1), ICW propagation is as well blocked because IP3 diffusion is much slower than its degradation." }, { "doi": "10.3389/fninf.2018.00020", "study": "Manninen et al. 2018 (Reproducibility of astrocyte models)", "value": "0 of 9 tested astrocyte models deposited in ModelDB by their original authors", "method": "Hand re-implementation from original publications; simulation-tool cross-comparison; reproducibility/replicability scoring", "metric": "canonical-model availability in public repositories", "study_system": "Re-implementation of nine canonical astrocyte Ca²⁺ models (including Li-Rinzel, De Young-Keizer, Lavrentovich-Hemkin, De Pittà 2009, Riera 2011)", "value_source_section": "3. Results > 3.2.2. Astrocyte models", "value_source_sentence": "None of the models were available in model repositories by the original authors." } ], "description": "Five fulltext computational-astrocyte papers in the corpus, each describing how a canonical Ca²⁺ oscillation model (Goldbeter 1990, De Young–Keizer 1992, Li–Rinzel 1994, De Pittà 2009) is adopted and parameterized. Each data_point is from a DIFFERENT paper (unique DOI). Synthesized across the five, the models use overlapping core parameters yet produce overly-regular deterministic oscillations that disagree with experimental 87 s astrocyte traces.", "comparison_id": "biophysical_ca2_models_parameter_comparison", "source_papers": [ "10.3389/fncel.2025.1536096", "10.3389/fncom.2018.00014", "10.1155/2016/7607924", "10.3389/fncom.2014.00045", "10.3389/fninf.2018.00020" ], "integrative_claim": "Across five independent computational studies the same ~2-3 variable CICR + IP3R-gating backbone (Li-Rinzel / De Young-Keizer / De Pittà ChI) is used with overlapping core parameters (Ca²⁺ threshold ~0.15–0.8 μM; IP3 flux floor ~0.1 μM·s⁻¹); yet when re-simulated over the 87 s experimental window the deterministic output remains regular and fails to reproduce the non-stationary astrocyte Ca²⁺ envelope, while the original code for most models is unavailable for independent replication. Closing the model-vs-experiment gap therefore requires (i) stochastic IP3R gating and (ii) shared/open parameter repositories." }, "section_id": "section_13_evidence_package", "source_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewAstrocytes/blob/1a55da0634a3bc04e5688792ed12141ce271d28e/evidence/section_13_evidence_package.json", "target_ref": "wiki_page:computationalreviewastrocytes-13", "review_repo": "ComputationalReviewAstrocytes", "section_ref": "wiki_page:computationalreviewastrocytes-13", "source_path": "evidence/section_13_evidence_package.json", "source_refs": [], "section_title": "Computational Models of Astrocyte–Neuron Interactions", "source_policy": { "mode": "public_source_pointer_with_short_context", "notes": [ "Local review repositories are read-only inputs.", "SciDEX stores paper metadata, structured evidence, file pointers, and short citation contexts; it does not copy full review prose." ], "source_commit_sha": "1a55da0634a3bc04e5688792ed12141ce271d28e", "source_repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewAstrocytes" }, "generation_status": "complete", "review_bundle_ref": "analysis_bundle:ab-029ee9411fe2", "origin_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewAstrocytes/blob/1a55da0634a3bc04e5688792ed12141ce271d28e/evidence/section_13_evidence_package.json", "commit_sha": "1a55da0634a3bc04e5688792ed12141ce271d28e", "created_by": "persona-jerome-lecoq-gbo-neuroscience", "repository_url": "https://github.com/AllenNeuralDynamics/ComputationalReviewAstrocytes" }