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Analysis of model-based and model-free CEST effect quantification methods for different medical applications

Foo LS, Yap WS, Hum YC, Manan HA, Tee YK

J Magn Reson, 2020 01;310:106648.
PMID: 31760147 DOI: 10.1016/j.jmr.2019.106648

Chemical exchange saturation transfer (CEST) magnetic resonance imaging (MRI) holds great potential to provide new metabolic information for clinical applications such as tumor, stroke and Parkinson's Disease diagnosis. Many active research and developments have been conducted to translate this emerging MRI technique for routine clinical applications. In general, there are two CEST quantification techniques: (i) model-free and (ii) model-based techniques. The reliability of these quantification techniques depends heavily on the experimental conditions and quality of the collected data. Errors such as noise may lead to misleading quantification results and thus inaccurate diagnosis when CEST imaging becomes a standard or routine imaging scan in the future. This paper investigates the accuracy and robustness of these quantification techniques under different signal-to-noise (SNR) levels and magnetic field strengths. The quantified CEST effect before and after adding random Gaussian White Noise using model-free and model-based quantification techniques were compared. It was found that the model-free technique consistently yielded larger average percentage error across all tested parameters compared to its model-based counterpart, and that the model-based technique could withstand SNR of about 3 times lower than the model-free technique. When applied on noisy brain tumor, ischemic stroke, and Parkinson's Disease clinical data, the model-free technique failed to produce significant differences between normal and abnormal tissue whereas the model-based technique consistently generated significant differences. Although the model-free technique was less accurate and robust, its simplicity and thus speed would still make it a good approximate when the SNR was high (>50) or when the CEST effect was large and well-defined. For more accurate CEST quantification, model-based techniques should be considered. When SNR was low (<50) and the CEST effect was small such as those acquired from clinical field strength scanners, which are generally 3T and below, model-based techniques should be considered over model-free counterpart to maintain an average percentage error of less than 44% even under very noisy condition as tested in this work.

Matched MeSH terms: Computer Simulation
Analysis of secondary structure predictions of dengue virus type 2 NS2B/NS3 against crystal structure to evaluate the predictive power of the in silico methods

Othman R, Wahab HA, Yusof R, Rahman NA

In Silico Biol. (Gedrukt), 2007;7(2):215-24.
PMID: 17688447

Multiple sequence alignment was performed against eight proteases from the Flaviviridae family using ClustalW to illustrate conserved domains. Two sets of prediction approaches were applied and the results compared. Firstly, secondary structure prediction was performed using available structure prediction servers. The second approach made use of the information on the secondary structures extracted from structure prediction servers, threading techniques and DSSP database of some of the templates used in the threading techniques. Consensus on the one-dimensional secondary structure of Den2 protease was obtained from each approach and evaluated against data from the recently crystallised Den2 NS2B/NS3 obtained from the Protein Data Bank (PDB). Results indicated the second approach to show higher accuracy compared to the use of prediction servers only. Thus, it is plausible that this approach is applicable to the initial stage of structural studies of proteins with low amino acid sequence homology against other available proteins in the PDB.

Matched MeSH terms: Computer Simulation*
Fulltext Analysis of thin plates with holes by using exact geometrical representation within XFEM

Perumal L, Tso CP, Leng LT

J Adv Res, 2016 May;7(3):445-52.
PMID: 27222749 DOI: 10.1016/j.jare.2016.03.004

This paper presents analysis of thin plates with holes within the context of XFEM. New integration techniques are developed for exact geometrical representation of the holes. Numerical and exact integration techniques are presented, with some limitations for the exact integration technique. Simulation results show that the proposed techniques help to reduce the solution error, due to the exact geometrical representation of the holes and utilization of appropriate quadrature rules. Discussion on minimum order of integration order needed to achieve good accuracy and convergence for the techniques presented in this work is also included.

Matched MeSH terms: Computer Simulation
Analysis on the effect of the distances and inclination angles between human head and mobile phone on SAR

Hossain MI, Faruque MR, Islam MT

Prog Biophys Mol Biol, 2015 Nov;119(2):103-10.
PMID: 25863147 DOI: 10.1016/j.pbiomolbio.2015.03.008

The aim of this paper is to investigate the effects of the distances between the human head and internal cellular device antenna on the specific absorption rate (SAR). This paper also analyzes the effects of inclination angles between user head and mobile terminal antenna on SAR values. The effects of the metal-glass casing of mobile phone on the SAR values were observed in the vicinity of the human head model. Moreover, the return losses were investigated in all cases to mark antenna performance. This analysis was performed by adopting finite-difference time-domain (FDTD) method on Computer Simulation Technology (CST) Microwave Studio. The results indicate that by increasing the distance between the user head and antenna, SAR values are decreased. But the increase in inclination angle does not reduce SAR values in all cases. Additionally, this investigation provides some useful indication for future design of low SAR mobile terminal antenna.

Matched MeSH terms: Computer Simulation
Analytical analysis of second-order Stokes wave in Brillouin ring fiber laser

Al-Asadi HA, Abu Bakar MH, Al-Mansoori MH, Adikan FR, Mahdi MA

Opt Express, 2011 Dec 5;19(25):25741-8.
PMID: 22273966 DOI: 10.1364/OE.19.025741

This paper details a theoretical modeling of Brillouin ring fiber laser which incorporates the interaction between multiple Brillouin Stokes signals. The ring cavity was pumped at several Brillouin pump (BP) powers and the output was measured through an optical coupler with various coupling ratios. The first-order Brillouin Stokes signal was saturated with the presence of the second-order Stokes signal in the cavity as a result of energy transfer between them. The outcome of the study found that the optimum point for the first-order Stokes wave performance is at laser power reduction of 10%. Resultantly, at the optimum output coupling ratio of 90%, the BFL was able to produce 19.2 mW output power at BP power and Brillouin threshold power of 60 and 21.3 mW respectively. The findings also exhibited the feasibility of the theoretical models application to ring-type Brillouin fiber laser of various design parameters.

Matched MeSH terms: Computer Simulation
Analytical and computational sliding wear prediction in a novel knee implant: a case study

Hussin MS, Fernandez J, Ramezani M, Kumar P, Kelly PA

Comput Methods Biomech Biomed Engin, 2020 Mar;23(4):143-154.
PMID: 31928215 DOI: 10.1080/10255842.2019.1709118

Osteoarthritis (OA) is a commonly occurring cartilage degenerative disease. The end stage treatment is Total Knee Arthroplasty (TKA), which can be costly in terms of initial surgery, but also in terms of revision knee arthroplasty, which is quite often required. A novel conceptual knee implant has been proposed to function as a reducer of stress across the joint surface, to extend the period of time before TKA becomes necessary. The objective of this paper is to develop a computational model which can be used to assess the wear arising at the implant articulating surfaces. Experimental wear coefficients were determined from physical testing, the results of which were verified using a semi-analytical model. Experimental results were incorporated into an anatomically correct computational model of the knee and implant. The wear-rate predicted for the implant was 27.74 mm3 per million cycles (MC) and the wear depth predicted was 1.085 mm/MC. Whereas the wear-rate is comparable to that seen in conventional knee implants, the wear depth is significantly higher than for conventional knee prostheses, and indicates that, in order to be viable, wear-rates should be reduced in some way, perhaps by using low-wear polymers.

Matched MeSH terms: Computer Simulation*
Analytical solution of reaction-diffusion equations for calcium wave propagation in a starburst amacrine cell

Poznanski RR

J Integr Neurosci, 2010 Sep;9(3):283-97.
PMID: 21064219

A reaction-diffusion model is presented to encapsulate calcium-induced calcium release (CICR) as a potential mechanism for somatofugal bias of dendritic calcium movement in starburst amacrine cells. Calcium dynamics involves a simple calcium extrusion (pump) and a buffering mechanism of calcium binding proteins homogeneously distributed over the plasma membrane of the endoplasmic reticulum within starburst amacrine cells. The system of reaction-diffusion equations in the excess buffer (or low calcium concentration) approximation are reformulated as a nonlinear Volterra integral equation which is solved analytically via a regular perturbation series expansion in response to calcium feedback from a continuously and uniformly distributed calcium sources. Calculation of luminal calcium diffusion in the absence of buffering enables a wave to travel at distances of 120 μm from the soma to distal tips of a starburst amacrine cell dendrite in 100 msec, yet in the presence of discretely distributed calcium-binding proteins it is unknown whether the propagating calcium wave-front in the somatofugal direction is further impeded by endogenous buffers. If so, this would indicate CICR to be an unlikely mechanism of retinal direction selectivity in starburst amacrine cells.

Matched MeSH terms: Computer Simulation
Anti-diarrheal activities of phytol along with its possible mechanism of action through in-vivo and in-silico models

Islam MT, Rahman MA, Saeed M, Ul-Haq Z, Alam MJ, Mondal M, et al.

Cell Mol Biol (Noisy-le-grand), 2020 Jun 25;66(4):243-249.
PMID: 32583783

Phytol (PHY), a chlorophyll-derived diterpenoid, exhibits numerous pharmacological properties, including antioxidant, antimicrobial, and anticancer activities. This study evaluates the anti-diarrheal effect of phytol (PHY) along with its possible mechanism of action through in-vivo and in-silico models. The effect of PHY was investigated on castor oil-induced diarrhea in Swiss mice by using prazosin, propranolol, loperamide, and nifedipine as standards with or without PHY. PHY at 50 mg/kg (p.o.) and all other standards exhibit significant (p < 0.05) anti-diarrheal effect in mice. The effect was prominent in the loperamide and propranolol groups. PHY co-treated with prazosin and propranolol was found to increase in latent periods along with a significant reduction in diarrheal section during the observation period than other individual or combined groups. Furthermore, molecular docking studies also suggested that PHY showed better interactions with the α- and β-adrenergic receptors, especially with α-ADR1a and β-ADR1. In the former case, PHY showed interaction with hydroxyl group of Ser192 at a distance of 2.91Å, while in the latter it showed hydrogen bond interactions with Thr170 and Lys297 with a distance of 2.65 and 2.72Å, respectively. PHY exerted significant anti-diarrheal effect in Swiss mice, possibly through blocking α- and β-adrenergic receptors.

Matched MeSH terms: Computer Simulation*
Anticipating local flaps closed-form solution on 3D face models using finite element method

Kwan Z, Khairu Najhan NN, Yau YH, Luximon Y, M Nor F

Int J Numer Method Biomed Eng, 2020 11;36(11):e3390.
PMID: 32735083 DOI: 10.1002/cnm.3390

A realistic three-dimensional (3D) computational model of skin flap closures using Asian-like head templates from two different genders, male and female, has been developed. The current study aimed to understand the biomechanics of the local flap designs along with the effect of wound closures on the respective genders. Two Asian head templates from opposite genders were obtained to use as base models. A third-order Yeoh hyperelastic model was adapted to characterize as skin material properties. A single layer composed of combined epidermis and dermis was considered, and the models were thickened according to respective anatomical positions. Each model gender was excised with a fixed defect size which was consequently covered by three different local flap designs, namely advancement, rotation, and rhomboid flaps. Post-operative simulation presented various scenarios of skin flap closures. Rotation and rhomboid flaps demonstrated maximal tension at the apex of the flap for both genders as well as advancement flap in the female face model. However, advancement flap closure in the male face model was presented otherwise. Yet, the deformation patterns and the peak tension of the discussed flaps were consistent with conventional local flap surgery. Moreover, male face models generated higher stresses compared to the female face models with a 70.34% mean difference. Overall, the skin flap operations were executed manually, and the designed surgery model met the objectives successfully while acknowledging the study limitations. NOVELTY FILE: 3D head templates were considered to address the gap as 3D face models were uncommonly employed in understanding the biomechanics of the local flaps realistically. Most of the existing studies focus on the 2D and 3D planar geometry in their models. As gender comparison has yet to be addressed, we intended to fill this gap by exploring the stress contours of the local flap designs in different genders. Create a 3D face model from two opposite genders which is capable of simulating closure of wounds using local flaps with a focus on advancement, rotation, and rhomboid flaps.

Matched MeSH terms: Computer Simulation
Fulltext Application of empirical mode decomposition with local linear quantile regression in financial time series forecasting

Jaber AM, Ismail MT, Altaher AM

ScientificWorldJournal, 2014;2014:708918.
PMID: 25140343 DOI: 10.1155/2014/708918

This paper mainly forecasts the daily closing price of stock markets. We propose a two-stage technique that combines the empirical mode decomposition (EMD) with nonparametric methods of local linear quantile (LLQ). We use the proposed technique, EMD-LLQ, to forecast two stock index time series. Detailed experiments are implemented for the proposed method, in which EMD-LPQ, EMD, and Holt-Winter methods are compared. The proposed EMD-LPQ model is determined to be superior to the EMD and Holt-Winter methods in predicting the stock closing prices.

Matched MeSH terms: Computer Simulation
Application of the linear interaction energy method (LIE) to estimate the binding free energy values of Escherichia coli wild-type and mutant arginine repressor C-terminal domain (ArgRc)-l-arginine and ArgRc-l-citrulline protein-ligand complexes

Asi AM, Rahman NA, Merican AF

J Mol Graph Model, 2004 Mar;22(4):249-62.
PMID: 15177077

Protein-ligand binding free energy values of wild-type and mutant C-terminal domain of Escherichia coli arginine repressor (ArgRc) protein systems bound to L-arginine or L-citrulline molecules were calculated using the linear interaction energy (LIE) method by molecular dynamics (MD) simulation. The binding behaviour predicted by the dissociation constant (K(d)) calculations from the binding free energy values showed preferences for binding of L-arginine to the wild-type ArgRc but not to the mutant ArgRc(D128N). On the other hand, L-citrulline do not favour binding to wild-type ArgRc but prefer binding to mutant ArgRc(D128N). The dissociation constant for the wild-type ArgRc-L-arginine complex obtained in this study is in agreement with reported experimental results. Our results also support the experimental data for the binding of L-citrulline to the mutant ArgRc(D128N). These showed that LIE method for protein-ligand binding free energy calculation could be applied to the wild-type and the mutant E. coli ArgRc-L-arginine and ArgRc-L-citrulline protein-ligand complexes and possibly to other transcriptional repressor-co-repressor systems as well.

Matched MeSH terms: Computer Simulation*
Appraisal of adaptive neuro-fuzzy computing technique for estimating anti-obesity properties of a medicinal plant

Kazemipoor M, Hajifaraji M, Radzi CW, Shamshirband S, Petković D, Mat Kiah ML

Comput Methods Programs Biomed, 2015 Jan;118(1):69-76.
PMID: 25453384 DOI: 10.1016/j.cmpb.2014.10.006

This research examines the precision of an adaptive neuro-fuzzy computing technique in estimating the anti-obesity property of a potent medicinal plant in a clinical dietary intervention. Even though a number of mathematical functions such as SPSS analysis have been proposed for modeling the anti-obesity properties estimation in terms of reduction in body mass index (BMI), body fat percentage, and body weight loss, there are still disadvantages of the models like very demanding in terms of calculation time. Since it is a very crucial problem, in this paper a process was constructed which simulates the anti-obesity activities of caraway (Carum carvi) a traditional medicine on obese women with adaptive neuro-fuzzy inference (ANFIS) method. The ANFIS results are compared with the support vector regression (SVR) results using root-mean-square error (RMSE) and coefficient of determination (R(2)). The experimental results show that an improvement in predictive accuracy and capability of generalization can be achieved by the ANFIS approach. The following statistical characteristics are obtained for BMI loss estimation: RMSE=0.032118 and R(2)=0.9964 in ANFIS testing and RMSE=0.47287 and R(2)=0.361 in SVR testing. For fat loss estimation: RMSE=0.23787 and R(2)=0.8599 in ANFIS testing and RMSE=0.32822 and R(2)=0.7814 in SVR testing. For weight loss estimation: RMSE=0.00000035601 and R(2)=1 in ANFIS testing and RMSE=0.17192 and R(2)=0.6607 in SVR testing. Because of that, it can be applied for practical purposes.

Matched MeSH terms: Computer Simulation
Fulltext Approximate Bayesian analysis of Drosophila melanogaster polymorphism data reveals a recent colonization of Southeast Asia

Laurent SJ, Werzner A, Excoffier L, Stephan W

Mol Biol Evol, 2011 Jul;28(7):2041-51.
PMID: 21300986 DOI: 10.1093/molbev/msr031

Southeast Asian populations of the fruit fly Drosophila melanogaster differ from ancestral African and derived European populations by several morphological characteristics. It has been argued that this morphological differentiation could be the result of an early colonization of Southeast Asia that predated the migration of D. melanogaster to Europe after the last glacial period (around 10,000 years ago). To investigate the colonization process of Southeast Asia, we collected nucleotide polymorphism data for more than 200 X-linked fragments and 50 autosomal loci from a population of Malaysia. We analyzed this new single nucleotide polymorphism data set jointly with already existing data from an African and a European population by employing an Approximate Bayesian Computation approach. By contrasting different demographic models of these three populations, we do not find any evidence for an early divergence between the African and the Asian populations. Rather, we show that Asian and European populations of D. melanogaster share a non-African most recent common ancestor that existed about 2,500 years ago.

Matched MeSH terms: Computer Simulation
Fulltext Approximating non linear higher order ODEs by a three point block algorithm

Rasedee AFN, Abdul Sathar MH, Othman KI, Hamzah SR, Ishak N

PLoS One, 2021;16(2):e0246904.
PMID: 33577619 DOI: 10.1371/journal.pone.0246904

Differential equations are commonly used to model various types of real life applications. The complexity of these models may often hinder the ability to acquire an analytical solution. To overcome this drawback, numerical methods were introduced to approximate the solutions. Initially when developing a numerical algorithm, researchers focused on the key aspect which is accuracy of the method. As numerical methods becomes more and more robust, accuracy alone is not sufficient hence begins the pursuit of efficiency which warrants the need for reducing computational cost. The current research proposes a numerical algorithm for solving initial value higher order ordinary differential equations (ODEs). The proposed algorithm is derived as a three point block multistep method, developed in an Adams type formulae (3PBCS) and will be used to solve various types of ODEs and systems of ODEs. Type of ODEs that are selected varies from linear to nonlinear, artificial and real life problems. Results will illustrate the accuracy and efficiency of the proposed three point block method. Order, stability and convergence of the method are also presented in the study.

Matched MeSH terms: Computer Simulation*
Fulltext Artificial Bee Colony algorithm in estimating kinetic parameters for yeast fermentation pathway

Ismail AM, Remli MA, Choon YW, Nasarudin NA, Ismail NN, Ismail MA, et al.

J Integr Bioinform, 2023 Jun 01;20(2).
PMID: 37341516 DOI: 10.1515/jib-2022-0051

Analyzing metabolic pathways in systems biology requires accurate kinetic parameters that represent the simulated in vivo processes. Simulation of the fermentation pathway in the Saccharomyces cerevisiae kinetic model help saves much time in the optimization process. Fitting the simulated model into the experimental data is categorized under the parameter estimation problem. Parameter estimation is conducted to obtain the optimal values for parameters related to the fermentation process. This step is essential because insufficient identification of model parameters can cause erroneous conclusions. The kinetic parameters cannot be measured directly. Therefore, they must be estimated from the experimental data either in vitro or in vivo. Parameter estimation is a challenging task in the biological process due to the complexity and nonlinearity of the model. Therefore, we propose the Artificial Bee Colony algorithm (ABC) to estimate the parameters in the fermentation pathway of S. cerevisiae to obtain more accurate values. A metabolite with a total of six parameters is involved in this article. The experimental results show that ABC outperforms other estimation algorithms and gives more accurate kinetic parameter values for the simulated model. Most of the estimated kinetic parameter values obtained from the proposed algorithm are the closest to the experimental data.

Matched MeSH terms: Computer Simulation
Artificial neural network modeling of the water quality index for Kinta River (Malaysia) using water quality variables as predictors

Gazzaz NM, Yusoff MK, Aris AZ, Juahir H, Ramli MF

Mar Pollut Bull, 2012 Nov;64(11):2409-20.
PMID: 22925610 DOI: 10.1016/j.marpolbul.2012.08.005

This article describes design and application of feed-forward, fully-connected, three-layer perceptron neural network model for computing the water quality index (WQI)(1) for Kinta River (Malaysia). The modeling efforts showed that the optimal network architecture was 23-34-1 and that the best WQI predictions were associated with the quick propagation (QP) training algorithm; a learning rate of 0.06; and a QP coefficient of 1.75. The WQI predictions of this model had significant, positive, very high correlation (r=0.977, p<0.01) with the measured WQI values, implying that the model predictions explain around 95.4% of the variation in the measured WQI values. The approach presented in this article offers useful and powerful alternative to WQI computation and prediction, especially in the case of WQI calculation methods which involve lengthy computations and use of various sub-index formulae for each value, or range of values, of the constituent water quality variables.

Matched MeSH terms: Computer Simulation*
Assessing agreement in measurements of orthodontic study models: Digital caliper on plaster models vs 3-dimensional software on models scanned by structured-light scanner

Wan Hassan WN, Othman SA, Chan CS, Ahmad R, Ali SN, Abd Rohim A

Am J Orthod Dentofacial Orthop, 2016 Nov;150(5):886-895.
PMID: 27871715 DOI: 10.1016/j.ajodo.2016.04.021

INTRODUCTION: In this study we aimed to compare measurements on plaster models using a digital caliper, and on 3-dimensional (3D) digital models, produced using a structured-light scanner, using 3D software.
METHODS: Fifty digital models were scanned from the same plaster models. Arch and tooth size measurements were made by 2 operators, twice. Calibration was done on 10 sets of models and checked using the Pearson correlation coefficient. Data were analyzed by error variances, repeatability coefficient, repeated-measures analysis of variance, and Bland-Altman plots.
RESULTS: Error variances ranged between 0.001 and 0.044 mm for the digital caliper method, and between 0.002 and 0.054 mm for the 3D software method. Repeated-measures analysis of variance showed small but statistically significant differences (P <0.05) between the repeated measurements in the arch and buccolingual planes (0.011 and 0.008 mm, respectively). There were no statistically significant differences between methods and between operators. Bland-Altman plots showed that the mean biases were close to zero, and the 95% limits of agreement were within ±0.50 mm. Repeatability coefficients for all measurements were similar.
CONCLUSIONS: Measurements made on models scanned by the 3D structured-light scanner were in good agreement with those made on conventional plaster models and were, therefore, clinically acceptable.

Matched MeSH terms: Computer Simulation*
Assessing regional left ventricular thickening dysfunction and dyssynchrony via personalized modeling and 3D wall thickness measurements for acute myocardial infarction

Khalid A, Lim E, Chan BT, Abdul Aziz YF, Chee KH, Yap HJ, et al.

J Magn Reson Imaging, 2019 04;49(4):1006-1019.
PMID: 30211445 DOI: 10.1002/jmri.26302

BACKGROUND: Existing clinical diagnostic and assessment methods could be improved to facilitate early detection and treatment of cardiac dysfunction associated with acute myocardial infarction (AMI) to reduce morbidity and mortality.
PURPOSE: To develop 3D personalized left ventricular (LV) models and thickening assessment framework for assessing regional wall thickening dysfunction and dyssynchrony in AMI patients.
STUDY TYPE: Retrospective study, diagnostic accuracy.
SUBJECTS: Forty-four subjects consisting of 15 healthy subjects and 29 AMI patients.
FIELD STRENGTH/SEQUENCE: 1.5T/steady-state free precession cine MRI scans; LGE MRI scans.
ASSESSMENT: Quantitative thickening measurements across all cardiac phases were correlated and validated against clinical evaluation of infarct transmurality by an experienced cardiac radiologist based on the American Heart Association (AHA) 17-segment model.
STATISTICAL TEST: Nonparametric 2-k related sample-based Kruskal-Wallis test; Mann-Whitney U-test; Pearson's correlation coefficient.
RESULTS: Healthy LV wall segments undergo significant wall thickening (P 50% transmurality) underwent remarkable wall thinning during contraction (thickening index [TI] = 1.46 ± 0.26 mm) as opposed to healthy myocardium (TI = 4.01 ± 1.04 mm). For AMI patients, LV that showed signs of thinning were found to be associated with a significantly higher percentage of dyssynchrony as compared with healthy subjects (dyssynchrony index [DI] = 15.0 ± 5.0% vs. 7.5 ± 2.0%, P

Matched MeSH terms: Computer Simulation
Assessment of bioethanol yield by S. cerevisiae grown on oil palm residues: Monte Carlo simulation and sensitivity analysis

Samsudin MD, Mat Don M

Bioresour Technol, 2015 Jan;175:417-23.
PMID: 25459850 DOI: 10.1016/j.biortech.2014.10.116

Oil palm trunk (OPT) sap was utilized for growth and bioethanol production by Saccharomycescerevisiae with addition of palm oil mill effluent (POME) as nutrients supplier. Maximum yield (YP/S) was attained at 0.464g bioethanol/g glucose presence in the OPT sap-POME-based media. However, OPT sap and POME are heterogeneous in properties and fermentation performance might change if it is repeated. Contribution of parametric uncertainty analysis on bioethanol fermentation performance was then assessed using Monte Carlo simulation (stochastic variable) to determine probability distributions due to fluctuation and variation of kinetic model parameters. Results showed that based on 100,000 samples tested, the yield (YP/S) ranged 0.423-0.501g/g. Sensitivity analysis was also done to evaluate the impact of each kinetic parameter on the fermentation performance. It is found that bioethanol fermentation highly depend on growth of the tested yeast.

Matched MeSH terms: Computer Simulation
Assessment of the nlmixr R package for population pharmacokinetic modeling: A metformin case study

Mak WY, Ooi QX, Cruz CV, Looi I, Yuen KH, Standing JF

Br J Clin Pharmacol, 2023 Jan;89(1):330-339.
PMID: 35976674 DOI: 10.1111/bcp.15496

AIM: nlmixr offers first-order conditional estimation (FOCE), FOCE with interaction (FOCEi) and stochastic approximation estimation-maximisation (SAEM) to fit nonlinear mixed-effect models (NLMEM). We modelled metformin's pharmacokinetic data using nlmixr and investigated SAEM and FOCEi's performance with respect to bias and precision of parameter estimates, and robustness to initial estimates.
METHOD: Compartmental models were fitted. The final model was determined based on the objective function value and inspection of goodness-of-fit plots. The bias and precision of parameter estimates were compared between SAEM and FOCEi using stochastic simulations and estimations. For robustness, parameters were re-estimated as the initial estimates were perturbed 100 times and resultant changes evaluated.
RESULTS: The absorption kinetics of metformin depend significantly on food status. Under the fasted state, the first-order absorption into the central compartment was preceded by zero-order infusion into the depot compartment, whereas for the fed state, the absorption into the depot was instantaneous followed by first-order absorption from depot into the central compartment. The means of relative mean estimation error (rMEE) ( ME E SAEM ME E FOCEi ) and rRMSE ( RMS E SAEM RMS E FOCEi ) were 0.48 and 0.35, respectively. All parameter estimates given by SAEM appeared to be narrowly distributed and were close to the true value used for simulation. In contrast, the distribution of estimates from FOCEi were skewed and more biased. When initial estimates were perturbed, FOCEi estimates were more biased and imprecise.
DISCUSSION: nlmixr is reliable for NLMEM. SAEM was superior to FOCEi in terms of bias and precision, and more robust against initial estimate perturbations.

Matched MeSH terms: Computer Simulation

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