A Dynamic Constraint-based Modelling (DCBM) Approach With Alternative Metabolic Objective Functions Predicts The impact of Oxidative Stress on Stored Red Blood Cells (RBCs)
Bibliographic record
Abstract
Mathematical metabolic modelling is a systematic endeavour to allow identifying the main causes of an observed metabolic change and to estimate the consequences of an imposed metabolic perturbation regarding a biosystem. Dynamic Constraint-based modelling (DCBM) has delivered promising results in metabolic engineering and in bioprocess design by providing mechanistically relevant systems-level knowledge of a network of bioreactions. Here, we seek to establish a DCBM approach that leverages convex optimization and nonlinear regression mathematical toolkit to estimate dynamic intracellular metabolic flux distributions in stored Red Blood Cells (RBCs) for transfusion purposes. First, we developed an ad-hoc metabolic network including 77 reactions and 74 metabolites, second, we adapted Flux Variability Analysis (FVA) technique to quantify the connection between exometabolomic dynamics and the dynamics of feasible intracellular reaction flux ranges. We have obtained fine-grained flux range dynamics of the intracellular reactions for the benchmark data published in (Bordbar et al., 2016). Then, we defined four objective functions regarding the accumulation of oxidative stress in stored RBCs for performing a dynamic Flux Balance Analysis (DFBA). In all four cases, time-resolved flux predictions were obtained respecting the imposed equality and inequality constraints. Last, we adapted a quadratic programming (QP) approach to calculate the Euclidean distance between the dynamic optimum flux vectors. The DCBM approach we have developed herein along with the developed metabolic network showed being suitable for the computational analysis of RBCs metabolic behaviour, and it is thought to be useful for other biosystems.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".