{
"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."
}