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Soft sensing of intracellular states for CHO cell bioprocessing with Ensemble Kalman Filters

Open access
Yu, Luxi, del Rio Chanona, Antonio, Kontoravdi, Cleo·2026·Journal of Process Control

Abstract

Abstract In biotherapeutic manufacturing, product quality such as glycosylation profile is typically assessed only after harvest, limiting opportunities for corrective action during cell culture operation. Intracellular nucleotide sugar donors (NSD) directly determine glycosylation outcomes but are rarely measured, even offline, due to analytical complexity and process disruption. As a result, quality-related decisions remain constrained to fixed operating strategies. This work introduces a model-based soft sensing framework to infer NSD concentrations from readily available extracellular measurements. A Bayesian state estimation approach based on the Ensemble Kalman Filter (EnKF) is developed to reconstruct unmeasured intracellular states during CHO cell culture. An imperfect kinetic process model is combined with noisy extracellular measurements, explicitly accounting for process variability and measurement uncertainty through ensemble-based propagation and updates. The framework is validated using four independent experiments with distinct feeding perturbations that are not used for model calibration. Although the open-loop model exhibited substantial mismatch for both extracellular metabolites and intracellular NSDs, EnKF assimilation of extracellular measurements corrected key metabolic profiles. Building on these corrected extracellular dynamics, the EnKF demonstrated robust estimation of a growth-determining amino acid, asparagine, from correlated extracellular states. Based on the improved extracellular and amino acid estimates, the framework further enabled reliable inference of intracellular NSDs across all experiments.

AI snapshot

Written from the paper’s full text.

TL;DR

This paper develops an Ensemble Kalman Filter (EnKF) soft sensor that infers unmeasured intracellular nucleotide sugar donors (NSDs) and asparagine in CHO cell culture from routine extracellular measurements. Across four independent fed-batch validation experiments, EnKF assimilation corrected extracellular metabolite profiles and enabled dynamic inference of NSDs, though NSDs remain structurally unobservable and their estimates depend on model structure and upstream state uncertainty.

Key findings

  • The EnKF achieved lower RMSE than the open-loop mechanistic model for every measured extracellular variable across all 4 validation datasets, with posterior bands containing most measurements and spread-to-error ratios near unity for well-determined states such as glutamine.
  • Asparagine, although unmeasured, had one of the highest empirical observability scores and was inferred robustly from coupled extracellular measurements; the open-loop model drifted low and fell close to zero by the end of every batch, while EnKF estimates stayed close to measured trajectories.
  • Intracellular NSDs were structurally unobservable under the routine measurement configuration, but EnKF still inferred them: UDP-GlcNAc improved most because it couples to well-corrected glutamine through a well-identified submodel; UDP-Glc was accurate in the mean but weakly constrained due to glucose structural mismatch; UDP-Gal was comparable to open-loop but gained calibrated uncertainty bands.
  • Ensemble size was selected as n = 100 from a sensitivity analysis over {25, 50, 100, 150, 200}, and each scenario was simulated 10 times with mean trajectories reported.

Methods

  • A two-component mechanistic model was used, coupling extracellular CHO cell culture behaviour with intracellular NSD metabolism; parameters were identified using 5 fed-batch experiments from an IgG-producing CHO-T127 cell line under different galactose and uridine supplementation strategies.
  • Validation used 4 additional independent fed-batch experiments not used for parametrisation, each with a distinct galactose and uridine feeding profile; EnKF performance was cross-validated by using one dataset as the sole tuning set and evaluating on the 3 held-out batches.
  • The EnKF represented uncertainty with an ensemble of state trajectories, applied state-wise process noise (multiplicative for measured states, additive for unmeasured states), and used ensemble cross-covariances to update unmeasured states indirectly; empirical observability was assessed with a simulation-based empirical observability Gramian.

Limitations

  • The paper states that the EnKF analysis step remains linear and Gaussian, so it is not a universal remedy for strong nonlinearity, and its accuracy depends on the ensemble forecast capturing dominant process nonlinearities.
  • The paper states that NSDs are structurally unobservable, so no estimator can recover them uniquely from measurements alone; inferred posterior distributions remain dependent on model structure and uncertainty specification.
  • The paper states that glucose innovations remained above the consistency target even at the noise cap, indicating a structural limitation of the coupled glucose/galactose-lactate description; future work could use dual state-parameter estimation or an explicit model-discrepancy term.
  • Evident from the text: validation used the same CHO-T127 cell line, culture medium, and operating conditions as calibration, so generalisation is demonstrated across feeding strategies rather than across cell lines or process configurations; NSD validation measurements were offline and not assimilated by the filter.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.jprocont.2026.103875

Cites

60 of 60 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

6 of 30 cited sources checked · 1 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    Two-step frameworks for indirect NSD inference rely on pseudo-steady-state assumptions and therefore do not explicitly capture the transient dynamics of intracellular NSD pools over the course of a fed-batch culture.

    “Although this approach enables indirect inference of NSDs from extracellular data and alleviates some parametrisation challenges, it relies on pseudo-steadystate assumptions.It therefore does not explicitly capture the transient dynamics of intracellular NSD pools over the course of a fed-batch culture.”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [27] Sha, 2019, Prediction of N-linked glycoform profiles of monoclonal antibody with extracellular metabolites and two-step intracellular models, Processes source

      The Introduction and §3.2 describe a two-step model that infers nucleotide-sugar availability from extracellular data using FBA and adjusts Golgi concentrations between cultures, rather than tracking intracellular pool concentrations over time. The Discussion says this reduces kinetic parameters, but our copy does not explicitly state a pseudo-steady-state assumption. It also says the model was applied only to the exponential phase and proposes extending it to the stationary phase common in fed-batch cultures, so the fed-batch scope is not established. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [28] Antonakoudis, 2021, Synergising stoichiometric modelling with artificial neural networks to predict antibody glycosylation patterns in Chinese hamster ovary cells, Comput. Chem. Eng. source
  • Premisecitation

    UDP-Gal is the immediate intracellular precursor for terminal galactosylation of N-linked glycans.

    “UDP-Gal is the immediate intracellular precursor for terminal galactosylation of N -linked glycans [49].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [49] Blondeel, 2018, Supplementing glycosylation: A review of applying nucleotide-sugar precursors to growth medium to affect therapeutic recombinant protein glycoform distributions, Biotech. Adv. source

      Section 2.1 (p. 6) describes nucleotide-sugars as glycosylation substrates, and Section 3.3.2 (p. 19) reports that galactose precursor feeding increases galactosylation. Figure 1 (p. 48) labels a UDP-Gal transporter, but the available text does not explicitly identify UDP-Gal as the immediate intracellular precursor for terminal galactosylation of N-linked glycans. (LLM, conf=0.80)

      Experimental — accuracy not yet measured
  • Premisecitation

    Nucleotide sugar donors (NSDs) serve as essential substrates for N-linked glycosylation, a critical quality attribute that strongly influences the safety, efficacy, and pharmacokinetics of recombinant protein products.

    “Specifically, nucleotide sugar donors (NSDs) serve as essential substrates for N -linked glycosylation, a critical quality attribute that strongly influences the safety, efficacy, and pharmacokinetics of recombinant protein products [11,12].”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [11] Del Val, 2016, A theoretical estimate for nucleotide sugar demand towards Chinese Hamster Ovary cellular glycosylation, Sci. Rep. source
    • cites [12] Van Landuyt, 2019, Customized protein glycosylation to improve biopharmaceutical function and targeting, Curr. Opin. Biotechnol. source
  • Findingown data

    The mechanistic model consistently overpredicted extracellular glutamine concentrations across all conditions.

    “the mechanistic model also consistently overpredicted extracellular glutamine concentrations across all conditions”
    Quote in the paperSubstantial claim
  • Findingown data

    Viable cell density, glucose, and ammonia exhibit consistently high Gramian scores, reflecting their strong dynamic coupling to the system through growth and death kinetics.

    “Viable cell density, glucose, and ammonia exhibit consistently high Gramian scores, reflecting their strong dynamic coupling to the system through growth and death kinetics.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. 15
  • May combine two claims. 56
  • The quote only partly states this claim. 2
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Asparagine plays a central metabolic role in mammalian cell culture, acting as a nitrogen donor for amino acid and nucleotide biosynthesis, supporting protein translation, and contributing to TCA cycle intermediates that sustain biomass growth and productivity.

    “Asparagine plays a central metabolic role in mammalian cell culture, acting as a nitrogen donor for amino acid and nucleotide biosynthesis, supporting protein translation, and contributing to TCA cycle intermediates that sustain biomass growth and productivity [48].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [48] Kirsch, 2022, Metabolic analysis of the asparagine and glutamine dynamics in an industrial Chinese hamster ovary fed-batch process, Biotechnol. Bioeng. source

      Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
  • May combine two claims.

    Interpretationcitation

    The EnKF cannot narrow the UDP-Glc band, since UDP-Glc is unobservable and its synthesis is modelled as a fixed function of extracellular glucose that neglects transport and the regulation of glycolytic flux.

    “The EnKF cannot narrow this band, since UDP-Glc is unobservable and its synthesis is modelled as a fixed function of extracellular glucose that neglects transport and the regulation of glycolytic flux [52].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [52] Maldonado, 2014, ATP/ADP ratio, the missed connection between mitochondria and the Warburg effect, Mitochondrion source

      The Introduction discusses glucose metabolism and the Conclusion discusses regulation of glycolysis by ATP/ADP ratios, but neither addresses the claimed UDP-Glc model. Searches for EnKF, UDP-Glc observability, and UDP-glucose synthesis found no passage supporting the asserted reason the band cannot narrow. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
  • May combine two claims.

    Premisecitation

    NSDs are synthesised intracellularly from extracellular metabolites such as glucose, glutamine, galactose, and uridine through a sequence of cytosolic enzymatic reactions, and are subsequently consumed in the Golgi apparatus during glycosylation.

    “NSDs are synthesised intracellularly from extracellular metabolites such as glucose, glutamine, galactose, and uridine through a sequence of cytosolic enzymatic reactions, and are subsequently consumed in the Golgi apparatus during glycosylation [20,21,25].”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites [20] Jimenez del Val, 2011, A dynamic mathematical model for monoclonal antibody N-linked glycosylation and nucleotide sugar donor transport within a maturing Golgi apparatus, Biotechnol. Prog. source
    • cites [21] Jedrzejewski, 2014, Towards controlling the glycoform: A model framework linking extracellular metabolites to antibody glycosylation, Int. J. Mol. Sci. source

      Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

      Experimental — accuracy not yet measured
    • cites [25] Kotidis, 2019, Model-based optimization of antibody galactosylation in CHO cell culture, Biotechnol. Bioeng. source
  • May combine two claims.

    Findingown data

    The mechanistic model systematically overestimated viable cell density for all feeding strategies, even though it was parametrised using data from the same cell line.

    “As shown in Fig. 4(a)-(d), the mechanistic model systematically overestimated viable cell density for all feeding strategies, even though it was parametrised using data from the same cell line.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Glucose is corrected in the mean, but its innovations remain far above the consistency target even at the noise cap.

    “Glucose is corrected in the mean, but its innovations remain far above the consistency target even at the noise cap, as reported in Supplementary Information C.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    UDP-Glc has the widest band of the reported NSDs, because the glucose spread propagates through the submodel.

    “As UDP-Glc is synthesised directly from glucose, this spread propagates through the submodel and gives UDP-Glc the widest band of the reported NSDs.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingnone given

    Glutamine carries the narrowest posterior band of the measured states, so its corrected trajectory is the most tightly constrained of the measured states.

    “Glutamine also carries the narrowest posterior band of the measured states, so its corrected trajectory is the most tightly constrained of the measured states.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingreasoning

    The UDP-GlcNAc uncertainty band remains wide, but the corrected estimate sits well within it and the residual overprediction is much reduced.

    “The uncertainty band remains wide, as for the other unobservable NSDs, but the corrected estimate sits well within it and the residual overprediction is much reduced.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    The width of the estimated UDP-Gal band scales with the size of the precursor pool: it remains narrow while UDP-Gal is low in early culture and broadens as the pool fills after the later galactose feeds.

    “The width of the estimated band scales with the size of the precursor pool.”
    • Also stated in: § 3.4.1. Galactosylation precursor dynamics: UDP-Gal · plain
      “It remains narrow while UDP-Gal is low in early culture and broadens as the pool fills after the later galactose feeds, so the reported confidence contracts and expands with the underlying concentration.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingcitation

    Uridine concentrations were quantified using HPLC and therefore exhibited lower measurement noise.

    “In contrast, uridine concentrations were quantified using HPLC [9] and therefore exhibited lower measurement noise.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [9] Del Val, 2013, An optimized method for extraction and quantification of nucleotides and nucleotide sugars from mammalian cells, Anal. Biochem. source
  • May combine two claims.

    Findingreasoning

    The posterior band includes the measurements throughout the culture, with most data points contained within the ±1σ envelope and a spread-to-error ratio close to unity.

    “The posterior band includes the measurements throughout the culture, with most data points contained within the ±1𝜎 envelope and a spread-to-error ratio close to unity.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    The open-loop model underpredicts UDP-Glc through the mid-culture phase, mirroring its underprediction of extracellular glucose.

    “The open-loop model underpredicts UDP-Glc through the mid-culture phase, mirroring its underprediction of extracellular glucose.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingnone given

    The uncertainty bands are narrowest where the estimate is most confident, as for well-determined states such as glutamine, and substantially wider for structurally mismatched ones such as glucose.

    “The uncertainty bands are narrowest where the estimate is most confident, as for well-determined states such as glutamine, and substantially wider for structurally mismatched ones such as glucose.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    The EnKF estimate of UDP-Gal is comparable to the open-loop prediction, because the mechanistic model already reproduces the measured trajectory and the assimilated galactose mainly keeps the estimate consistent with it; the filter adds a calibrated uncertainty band rather than a much more accurate mean.

    “The EnKF estimate of UDP-Gal is comparable to the open-loop prediction, as shown in Fig. 6(a)-(d), because the mechanistic model already reproduces the measured trajectory and the assimilated galactose mainly keeps the estimate consistent with it.”
    • Also stated in: § 3.4.3. Branching precursor with strong inferability: UDP-GlcNAc · plain
      “UDP-Gal is already reproduced well by the open-loop model and gains a calibrated uncertainty band rather than much more accurate mean.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    Correcting the glutamine level through assimilation removes most of the UDP-GlcNAc bias, and the EnKF estimate tracks the measurements well across all 4 datasets.

    “Correcting the glutamine level through assimilation removes most of this bias, and the EnKF estimate tracks the measurements well across all 4 datasets.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    As asparagine is observable, the measurements constrain the estimate and its uncertainty band stays tight, in contrast to the unobservable NSDs.

    “As asparagine is observable, the measurements constrain the estimate and its uncertainty band stays tight, in contrast to the unobservable NSDs examined next.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    UDP-Gal receives essentially the same additive process noise but is driven by the better-behaved galactose, so its band is correspondingly narrower than that of UDP-Glc.

    “UDP-Gal receives essentially the same additive process noise but is driven by the better-behaved galactose, so its band is correspondingly narrower.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    The EnKF estimates for galactose aligned closely with experimental measurements while avoiding overfitting of spurious fluctuations, particularly in regions where apparent concentration increases occurred in the absence of feeding events.

    “Fig. 4(e)-(h) show the EnKF estimates for galactose aligned closely with experimental measurements while avoiding overfitting of spurious fluctuations, particularly in regions where apparent concentration increases occurred in the absence of feeding events.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingnone given

    The EnKF adjusted glucose trajectories, but glucose retains the widest posterior band of the measured states and the filter reports lower confidence than for other states.

    “The EnKF adjusted glucose trajectories accordingly, although glucose retains the widest posterior band of the measured states and the filter reports lower confidence comparing to other states.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingreasoning

    The UDP-Glc estimate is the least certain of the reported NSDs, and this uncertainty is inherited from glucose.

    “The UDP-Glc estimate is the least certain of the reported NSDs, and this uncertainty is inherited from glucose.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingreasoning

    The open-loop model overpredicts UDP-GlcNAc across all feeding strategies, increasingly so towards the end of culture, following its overprediction of glutamine.

    “The open-loop model overpredicts UDP-GlcNAc across all feeding strategies, increasingly so towards the end of culture, following its overprediction of glutamine.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    The EnKF compensates for the mismatch by assimilating viable cell density measurements, recovering growth trajectories that closely follow the experimental profiles.

    “The EnKF effectively compensates for this mismatch by assimilating viable cell density measurements, recovering growth trajectories that closely follow the experimental profiles.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    For both galactose and uridine, the ±2σ envelope contains most of the experimental data.

    “For both states the ±2𝜎 envelope contains most of the experimental data.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingreasoning

    Assay differences are visible in the posterior bands: the galactose band is broad and the filter follows the underlying trend rather than the scattered readings, while the more precise uridine measurements yield a narrower band.

    “These assay differences are visible in the posterior bands.The galactose band is broad, and the filter follows the underlying trend rather than the scattered readings.The more precise uridine measurements yield a narrower band.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Measurement assimilation via the EnKF corrected the glutamine deviations and recovered trajectories that closely matched the observed profiles.

    “Measurement assimilation via the EnKF corrected these deviations and recovered trajectories that closely matched the observed profiles.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    The open-loop model reproduces asparagine early in culture but drifts progressively low thereafter, falling close to zero by the end of every batch, whereas the measured concentration declines only gradually.

    “the open-loop model reproduces asparagine early in culture but drifts progressively low thereafter, falling close to zero by the end of every batch, whereas the measured concentration declines only gradually”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    The NSDs' uncertainty bands are wide, in contrast to the narrow band obtained for observable asparagine.

    “Their uncertainty bands are therefore wide, in contrast to the narrow band obtained for observable asparagine.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    For the directly measured extracellular states, the EnKF corrected the systematic biases of the open-loop model and attenuated measurement noise, achieving a lower error than the open-loop model for every variable and across all datasets.

    “For the directly measured extracellular states, the EnKF corrected the systematic biases of the open-loop model and attenuated measurement noise, achieving a lower error than the open-loop model for every variable and across all datasets.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisereasoning

    The system has a strictly unidirectional information structure in which extracellular states drive NSD synthesis, while variations in NSD concentrations do not propagate measurable effects back to the extracellular environment.

    “This system structure reflects an inherent biological property characterised by a strictly unidirectional information structure, in which extracellular states drive NSD synthesis, while variations in NSD concentrations do not propagate measurable effects back to the extracellular environment.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationreasoning

    The corrections applied to the measured states point to an underlying model bias, which takes a parametric and a structural form.

    “The corrections applied to the measured states points to an underlying model bias and takes two forms.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    A simulation-based observability assessment based on the empirical observability Gramian was adopted.

    “To address these challenges, a simulation-based observability assessment based on the empirical observability Gramian was adopted.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationreasoning

    UDP-GlcNAc is the NSD that benefits most from assimilation and is reconstructed most accurately, because it is coupled to well-tracked glutamine through a well-identified submodel.

    “making UDP-GlcNAc the NSD that benefits most from assimilation”
    • Also stated in: § 4. Conclusions · plain
      “UDP-GlcNAc, coupled to welltracked glutamine through a well-identified submodel, is reconstructed most accurately.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    UDP-GlcNAc is a branching precursor in N-linked glycosylation and acts as the substrate for several branching and modification reactions.

    “UDP-GlcNAc is a branching precursor in N -linked glycosylation and acts as the substrate for several branching and modification reactions [53,54].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [53] Krambeck, 2005, A mathematical model of N-linked glycosylation, Biotechnol. Bioeng. source
    • cites [54] Kontoravdi, 2018, Computational tools for predicting and controlling the glycosylation of biopharmaceuticals, Curr. Opin. Chem. Eng. source
  • May combine two claims.

    Interpretationreasoning

    The confidence of an NSD estimate depends in addition on the uncertainty of its driving state, so an input that is tracked in the mean but structurally mismatched, such as glucose, yields an accurate but weakly constrained NSD, as seen for UDP-Glc.

    “The confidence of an estimate depends in addition on the uncertainty of its driving state, so an input that is tracked in the mean but structurally mismatched, such as glucose, yields an accurate but weakly constrained NSD, as seen for UDP-Glc.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The Ensemble Kalman Filter (EnKF) is a Monte Carlo-based extension of the Kalman Filter designed for nonlinear and high-dimensional systems.

    “The EnKF is a Monte Carlo-based extension of the Kalman Filter designed for nonlinear and high-dimensional systems [43].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [43] Evensen, 1994, Sequential data assimilation with a nonlinear quasi-geostrophic model using Monte Carlo methods to forecast error statistics, J. Geophys. Res. source
  • May combine two claims.

    Interpretationreasoning

    The ensemble-based formulation ensures that uncertainty propagation remains consistent with the nonlinear process dynamics, allowing variability in observable extracellular metabolite states to be transmitted to intracellular NSD concentrations through mechanistic coupling, without imposing spurious linear sensitivity.

    “This ensemble-based formulation ensures that uncertainty propagation remains consistent with the nonlinear process dynamics, allowing variability in observable extracellular metabolite states to be transmitted to intracellular NSD concentrations through mechanistic coupling, without imposing spurious linear sensitivity.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisecitation

    UDP-GlcNAc synthesis kinetics were well identified in the original calibration, since UDP-GlcNAc is chemically stable and comparatively reliable to measure.

    “The result is reinforced by the fidelity of the UDP-GlcNAc submodel, since UDP-GlcNAc is chemically stable and comparatively reliable to measure [55], so its synthesis kinetics were well identified in the original calibration.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [55] Sugiura, 2007, MS analysis of chondroitin polymerization: Effects of Mn2+ ions on the stability of UDP-sugars and chondroitin synthesis, Anal. Biochem. source
  • May combine two claims.

    Interpretationown data

    The EnKF does not overcome the structural unobservability of NSDs, and the inferred posterior distributions remain dependent on model structure and uncertainty specification.

    “The EnKF does not overcome the structural unobservability of NSDs, and the inferred posterior distributions remain dependent on model structure and uncertainty specification.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationreasoning

    UDP-Glc is accurate in the mean while weakly constrained, with its confidence limited by the upstream uncertainty in glucose.

    “UDP-Glc is therefore accurate in the mean while weakly constrained, with its confidence limited by the upstream uncertainty in glucose.”
    • Also stated in: § 3.4.3. Branching precursor with strong inferability: UDP-GlcNAc · plain
      “UDP-Glc is corrected in the mean through the recovered glucose concentration but inherits the uncertainty of the structurally mismatched glucose state, so its estimate is accurate yet weakly constrained.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationreasoning

    The progressive underestimation of asparagine by the open-loop model is a downstream signature of the growth bias seen in the measured states, pointing to overestimated growth and asparagine-uptake parameters.

    “Asparagine uptake scales with the viable cell density, so this drift is a downstream signature of the growth bias seen in the measured states.”
    • Also stated in: § 4. Conclusions · plain
      “The progressive underestimation of asparagine by the open-loop model is a downstream signature of the growth bias, since the overpredicted cell growth overconsumes the pool, and assimilation of the coupled measurements removes it.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Asparagine uptake scales with the viable cell density.
  • May combine two claims.

    Interpretationreasoning

    The higher-than-predicted glucose accumulation is consistent with the reduced cell growth observed experimentally, compounded by galactose and glucose both being supplied to the culture.

    “This behaviour is consistent with the reduced cell growth observed experimentally, compounded by galactose and glucose are both supplied to the culture.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Each scenario was simulated 10 times and the mean trajectory was reported.

    “Each scenario was simulated 10 times and the mean trajectory was reported, ensuring repeatability while preserving the stochastic nature of the EnKF.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Premisenone given

    The EnKF represents state uncertainty through an ensemble of full nonlinear system trajectories, and the sample covariance of the ensemble provides a Monte Carlo approximation of the evolving state uncertainty.

    “Instead of the Jacobian-based local linearisation and analytical covariance propagation of the EKF, the EnKF represents state uncertainty through an ensemble of full nonlinear system trajectories.The sample covariance of the ensemble provides a Monte Carlo approximation of the evolving state uncertainty.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationreasoning

    The overprediction of viable cell density most plausibly reflects an overestimated maximum specific growth rate that propagates to the coupled central-carbon states, since the model was calibrated on lower-passage cultures.

    “The model was calibrated on lower-passage cultures, so the overprediction of viable cell density most plausibly reflects an overestimated maximum specific growth rate that propagates to the coupled central-carbon states.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    The NSDs are structurally unobservable, a limitation that no estimator can overcome by itself.

    “As the observability analysis shows, they are structurally unobservable, a limitation that no estimator can overcome by itself.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Study design and conductcitation

    Each filter was tuned on a single batch and evaluated on the 3 held-out batches, whose feeding strategies span the galactose and uridine design space.

    “Each filter was tuned on a single batch and evaluated on the 3 held-out batches, whose feeding strategies span the galactose and uridine design space [26].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [26] Kotidis, 2019, Constrained global sensitivity analysis for bioprocess design space identification, Comput. Chem. Eng. source
  • May combine two claims.

    Interpretationreasoning

    In the model, asparagine is tightly coupled to the specific growth rate, which in turn governs viable cell density, protein synthesis, and the uptake and secretion of extracellular metabolites.

    “In the model, asparagine is tightly coupled to the specific growth rate, which in turn, governs viable cell density, protein synthesis, and the uptake and secretion of extracellular metabolites.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisecitation

    Under galactose supplementation, reduced glucose uptake leads to elevated extracellular glucose concentrations and altered intracellular precursor dynamics.

    “Under galactose supplementation, reduced glucose uptake leads to elevated extracellular glucose concentrations and altered intracellular precursor dynamics [47].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [47] Gramer, 2011, Modulation of antibody galactosylation through feeding of uridine, manganese chloride, and galactose, Biotechnol. Bioeng. source
  • May combine two claims.

    Interpretationreasoning

    UDP-Gal is synthesised directly from extracellular galactose and is therefore the NSD most closely coupled to an assimilated measurement.

    “UDP-Gal is synthesised directly from extracellular galactose and is therefore the NSD most closely coupled to an assimilated measurement.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. The quote only partly states this claim.

    Study design and conductreasoning

    The measured-state coefficients of variation were fixed by a filter-consistency criterion requiring the normalised innovation variance to equal unity.

    “The measured-state coefficients of variation are fixed by a filterconsistency criterion.At each measurement time the innovation and its predicted covariance are”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Study design and conductown data

    The performance of the EnKF-based estimation framework was evaluated using 4 additional fed-batch experiments that were not used during model parametrisation.

    “The performance of the EnKF-based estimation framework was evaluated using 4 additional fed-batch experiments that were not used during model parametrisation.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisecitation

    The EKF relies on Jacobian-based linearisation of both the process and measurement models to propagate state covariances and compute correction Kalman gains; when unmeasured states do not influence output measurements, the corresponding sensitivities vanish, leading to degenerate or ill-conditioned covariance updates.

    “The EKF relies on Jacobian-based linearisation of both the process and measurement models to propagate state covariances and compute the correction Kalman gains [45].When the unmeasured states do not influence the output measurements, the corresponding sensitivities vanish, leading to degenerate or illconditioned covariance updates.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [45] Simon, 2006 source
  • May combine two claims.

    Study design and conductown data

    The validation experiments employed the same CHO-T127 cell line, culture medium, and operating conditions as those used for model calibration.

    “These experiments were conducted independently but employed the same CHO-T127 cell line, culture medium, and operating conditions as those used for model calibration.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisereasoning

    The EnKF represents uncertainty using an ensemble of state trajectories that are evolved forward through the nonlinear process model and updated sequentially as measurements become available.

    “Instead of propagating state covariances analytically, the EnKF represents uncertainty using an ensemble of state trajectories that are evolved forward through the nonlinear process model and updated sequentially as measurements become available.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    When galactose is supplemented, carbon flux can be redirected towards central energy metabolism, reducing reliance on glucose as the primary carbon and energy source.

    “When galactose is supplemented, carbon flux can be redirected towards central energy metabolism, reducing reliance on glucose as the primary carbon and energy source.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [25] Kotidis, 2019, Model-based optimization of antibody galactosylation in CHO cell culture, Biotechnol. Bioeng. source
    • cites [47] Gramer, 2011, Modulation of antibody galactosylation through feeding of uridine, manganese chloride, and galactose, Biotechnol. Bioeng. source
  • May combine two claims.

    Interpretationreasoning

    The EnKF requires neither the sigma-point tuning of the UKF nor the repeated optimisation of moving-horizon estimation, and it scales to higher dimensions more favourably than particle filtering.

    “It thereby requires neither the sigma-point tuning of the UKF nor the repeated optimisation of moving-horizon estimation, and it scales to higher dimensions more favourably than particle filtering.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisecitation

    UDP-Glc provides a direct link between central carbon metabolism and glycosylation, primarily governed by extracellular glucose availability.

    “UDP-Glc provides a direct link between central carbon metabolism and glycosylation, primarily governed by extracellular glucose availability [51].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [51] Sha, 2019, An investigation of nucleotide sugar dynamics under the galactose supplementation in CHO cell culture, Process Biochem. source
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    The measurement-noise covariance was set directly from the data as the experimental-triplicate variance, pooled across the 4 datasets, and was never fitted to the filter residuals.

    “The measurement-noise covariance is set directly from the data as the experimental-triplicate variance, pooled across the 4 datasets.This variance reflects measurement precision and is never fitted to the filter residuals.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductown data

    The complete tuning procedure was cross-validated across the 4 fed-batch datasets, with each fold using one dataset as the sole tuning set and applying the calibrated filter to the 3 held-out batches.

    “The complete procedure is cross-validated across the 4 fed-batch datasets.In each fold, one dataset serves as the sole tuning set and the calibrated filter is applied to the 3 held-out batches.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    Each validation experiment applied a distinct galactose and uridine supplementation profile, selected to span a design space constrained by requirements on product titre and galactosylation quality.

    “Each experiment applied a distinct galactose and uridine supplementation profile, selected to span a design space constrained by requirements on product titre and galactosylation quality, as reported in [26].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [26] Kotidis, 2019, Constrained global sensitivity analysis for bioprocess design space identification, Comput. Chem. Eng. source
  • May combine two claims. The quote only partly states this claim.

    Study design and conductown data

    The unmeasured-state additive variances were calibrated to achieve near-nominal coverage and a spread-to-error ratio of order unity for the states that carry validation measurements.

    “The scale factor is selected by calibrating the resulting uncertainty band, so as to achieve near-nominal coverage and a spread-to-error ratio of order unity for the states that carry validation measurements.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Five datasets were used exclusively for parametrisation of the mechanistic model prior to its integration with the EnKF.

    “Five datasets were used exclusively for parametrisation of the mechanistic model prior to its integration with the EnKF.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationreasoning

    The difference in observability between uridine and galactose arises from model structure: uridine enters the specific death rate and growth inhibition term, while galactose influences dynamics only indirectly through modulation of the specific glucose uptake rate.

    “This difference arises from model structure.Uridine enters the specific death rate directly (Eq.( 24), Supplementary Information A) and also the growth inhibition term (Eq.( 23), Supplementary Information A), so its perturbations propagate rapidly through the viable cell density and all growth-coupled states.Galactose, by contrast, influences the dynamics only indirectly through modulation of the”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationreasoning

    In practice, uncertainty in NSD states accumulates without meaningful correction, while linearisation errors introduced at each update step are not dissipated by measurement feedback, resulting in numerical instability or divergence.

    “In practice, uncertainty in NSD states accumulates without meaningful correction, while linearisation errors introduced at each update step are not dissipated by measurement feedback, resulting in numerical instability or divergence.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    UDP-Gal provides the mechanistic link between extracellular galactose and uridine supplementation and galactosylation, a key quality attribute of monoclonal antibodies.

    “It provides the mechanistic link between extracellular galactose and uridine supplementation and galactosylation, a key quality attribute of monoclonal antibodies [13,50].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [13] Hodoniczky, 2005, Control of recombinant monoclonal antibody effector functions by Fc N-glycan remodeling in vitro, Biotechnol. Prog. source
    • cites [50] Bheemareddy, 2019, Effect of the total galactose content on complement-dependent cytotoxicity of the therapeutic anti-CD20 IgG1 antibodies under temperature stress conditions, J. Carbohydr. Chem. source
  • May combine two claims.

    Interpretationreasoning

    Asparagine is a viable soft-sensing target, and the observability analysis offers a principled basis for selecting such estimable states.

    “Asparagine is thus a viable soft-sensing target, and the observability analysis offers a principled basis for selecting such estimable states.”
    Quote in the paperSubstantial claim
66 of 66
  • The authors state this as an assumption.

    Only a limited set of routinely measured extracellular metabolites is accessible.

    “under the assumption that only a limited set of routinely measured extracellular metabolites is accessible”
  • The paper relies on this without support.

    Glucose availability directly influences the synthesis rates of intracellular precursor pools that support glycosylation.

    “as glucose availability directly influences the synthesis rates of intracellular precursor pools that support glycosylation”
  • The authors state this as an assumption.

    The model assumes a direct relationship between extracellular and intracellular glutamine, with intracellular glutamine entering the rate expressions governing the synthesis of NSD.

    “the model assumes a direct relationship between extracellular and intracellular glutamine, with intracellular glutamine entering rate expressions governing the synthesis of NSD”
  • The paper relies on this without support.

    Asparagine uptake scales with the viable cell density.

    “Asparagine uptake scales with the viable cell density”
4 of 4

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Measurement noise is counted twice in the innovation covariance

    Major

    Equation (13) defines the predicted-measurement covariance with measurement noise R already added. Equation (16) adds R to that covariance again when defining the innovation covariance used for filter-consistency tuning.

1 of 1

Cites

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Authors
Yu, L., del Rio Chanona, A., & Kontoravdi, C.
Affiliations
Imperial College London (GB)
Corresponding author
Kontoravdi, Cleo
Venue
Journal of Process Control
Publisher
Elsevier BV
Published
2026-12
Volume
168
Pages
103875
ISSN
0959-1524 (ISSN-L)
OpenAlex
W7162762797
Cited by
0
References
55
FWCI
0.00
Type
journal article
Language
en
Open access
Locations
  • Journal of Process Control (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • Spiral (Imperial College London) (publishedVersion, cc-by)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Viral Infectious Diseases and Gene Expression in Insects
  • Physical Sciences › Engineering › Control and Systems Engineering › Control Systems and Identification
  • Physical Sciences › Engineering › Control and Systems Engineering › Fault Detection and Control Systems
Keywords
soft sensing, CHO cell culture, glycosylation, ensemble Kalman filter, Bayesian state estimation, asparagine, amino acid metabolism, data assimilation, bioprocess control

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-11-05.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-11-05.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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