Journal: bioRxiv

Article Title: A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience

doi: 10.1101/2020.11.17.385203

Figure Lengend Snippet: Simulations in identical conditions in both MATLAB ® SimBiology ® and COPASI yielded almost identical results. (A) Inputs used in both simulators. The calcium input is kept constant at 4 s for all simulations and dopamine input time is varied from time 0 to 8 s at every one second. The difference from the previous simulations is in the calcium input which, for the sake of simplicity, is represented by a double exponential spike. (B) and (C) show substrate phosphorylation curves analogous to , the red line represents results obtained in MATLAB ® and blue line results from simulations in COPASI.

Article Snippet: For the model and data storage we have chosen the SBtab format which can be easily read and modified by both modelers and experimentalists, and can be converted into other formats, e.g. SBML, MATLAB ® SimBiology ® or MOD.

Techniques:

Journal: Pharmaceutics

Article Title: Physiologically Based Pharmacokinetic Modeling in Neonates: Current Status and Future Perspectives

doi: 10.3390/pharmaceutics15122765

Figure Lengend Snippet: Neonatal PBPK modeling studies.

Article Snippet: [ ] , Dolutegravir , MATLAB SimBiology , 1. Recommended regimen for neonates: Day 1–20 = 5 mg every 48 h (q48h); Day 21–28 = 5 mg every 24 h (q24h). 2. If the mother has taken dolutegravir 2–24 h before delivery, the first dose for the newborn may be delayed until 24–48 h after birth..

Techniques: Injection, Concentration Assay, Clinical Proteomics, Dissolution, Quantitative Proteomics, Activity Assay, Expressing, In Vitro, In Vivo, Modification, Inhibition, Recombinant, Software

Journal: Biomaterials science

Article Title: Toward Reducing Biomaterials Antigenic Potential: A Miniaturized Fc-Binding Domain for Local Deposition of Antibodies

doi: 10.1039/c8bm01220b

Figure Lengend Snippet: Simulation of antibody in footpad injection depot. (a) One-compartment model diagramed using the Matlab Simbiology module (2017a) with the simulations governed by the equations described in Methods and Materials. Since it was assumed that no other anatomical structure or physiological mechanism was involved in the clearance, the depot is the single compartment in which the gel was injected, with “Ab_Z15EAK” representing IgG800 complexed with Z15_EAK/EAK coacervate, “Ab” representing dissociated IgG800, and “Z15EAK” representing Z15_EAK and EAK (which were assumed to remain always in the depot); reaction_1 represents reversible binding (kon and koff) between antibody and Z15, and reaction_2 represents elimination of antibody from the depot (kel); (b) Fitting of in vivo decay data in Fig. 6 to first-order elimination model to obtain kel; (d) Simulated profiles of the complex, Z15_EAK/EAK composite, and free antibody using Kd determined in ITC and the microplate assay. AUC was calculated using a trapezoidal numerical integration function in Matlab.

Article Snippet: Modeling and simulations Matlab 2017b with a Simbiology module was utilized to simulate concentration of unbound IgG upon footpad injection with Z15_EAK/EAK.

Techniques: Injection, Binding Assay, In Vivo