Techno-economic process modelling and Monte Carlo simulation data of uncertainty quantification in field-grown plant-based manufacturing.
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ABSTRACT:
SUBMITTER: McNulty MJ
PROVIDER: S-EPMC8405912 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND: Exposure to air pollution is associated with a short-term increase in mortality, and this field has begun to focus on health impact assessment. OBJECTIVES: Our aim was to estimate the impact of PM10 on mortality within 2 days from the exposure in the Italian region of Lombardy for the year 2007, at the municipality level, examining exposure entailed by daily intermunicipality commuting and accounting for uncertainty propagation. METHODS: We combined data from different sources to derive probabilistic distributions for all input quantities used to calculate attributable deaths (mortality rates, PM10 concentrations, estimated PM10 effects, and commuting flows) and applied a Monte Carlo procedure to propagate uncertainty and sample the distribution of attributable deaths for each municipality. RESULTS: We estimated that annual average PM10 concentrations above the World Health Organization-recommended threshold of 20 ?g/m3 were responsible for 865 short-term deaths (80% credibility interval: 475, 1,401), 26% of which were attributable to PM10 above the European Union limit of 40 ?g/m3. Reducing annual average PM10 concentrations > 20 ?g/m3 by 20% would have reduced the number of attributable deaths by 36%. The largest estimated impacts were along the basin of the Po River and in the largest cities. Commuting contributed to the spatial distribution of the estimated impact. CONCLUSIONS: Our estimates, which incorporated uncertainty quantification, indicate that the short-term impact of PM10 on mortality in Lombardy in 2007 was notable, and that reduction in air pollution would have had a substantial beneficial effect on population health. Using commuting data helped to identify critical areas for prioritizing intervention.
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Project description:The typical experimental procedure for testing stress corrosion cracking initiation involves an interval-censored reliability test. Based on these test results, the parameters of a Weibull distribution, which is a widely accepted crack initiation model, can be estimated using maximum likelihood estimation or median rank regression. However, it is difficult to determine the appropriate number of test specimens and censoring intervals required to obtain sufficiently accurate Weibull estimators. In this study, we compare maximum likelihood estimation and median rank regression using a Monte Carlo simulation to examine the effects of the total number of specimens, test duration, censoring interval, and shape parameters of the true Weibull distribution on the estimator uncertainty. Finally, we provide the quantitative uncertainties of both Weibull estimators, compare them with the true Weibull parameters, and suggest proper experimental conditions for developing a probabilistic crack initiation model through crack initiation tests.
| S-EPMC5456946 | biostudies-literature
Project description:The invention and advancement of biological microscopy depends critically on an ability to accurately simulate imaging of complex biological structures embedded within complex scattering media. Unfortunately no technique exists for rigorous simulation of the complete imaging process, including the source, instrument, sample and detector. Monte-Carlo modelling is the gold standard for the modelling of light propagation in tissue, but is somewhat laborious to implement and does not incorporate the rejection of scattered light by the microscope. On the other hand microscopes may be rigorously and rapidly modelled using commercial ray-tracing software, but excluding the interaction with the biological sample. We report a hybrid Monte-Carlo optical ray-tracing technique for modelling of complete imaging systems of arbitrary complexity. We make the software available to enable user-friendly and rigorous virtual prototyping of biological microscopy of arbitrary complexity involving light scattering, fluorescence, polarised light propagation, diffraction and coherence. Examples are presented for the modelling and optimisation of representative imaging of neural cells using light-sheet and micro-endoscopic fluorescence microscopy and imaging of retinal vasculature using confocal and non-confocal scanning-laser ophthalmoscopes.
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Project description:In this study, we apply four Monte Carlo simulation methods, namely, Monte Carlo, quasi-Monte Carlo, multilevel Monte Carlo and multilevel quasi-Monte Carlo to the problem of uncertainty quantification in the estimation of the average travel time during the transport of particles through random heterogeneous porous media. We apply the four methodologies to a model problem where the only input parameter, the hydraulic conductivity, is modelled as a log-Gaussian random field by using direct Karhunen-Loéve decompositions. The random terms in such expansions represent the coefficients in the equations. Numerical calculations demonstrating the effectiveness of each of the methods are presented. A comparison of the computational cost incurred by each of the methods for three different tolerances is provided. The accuracy of the approaches is quantified via the mean square error.
| S-EPMC5579089 | biostudies-literature
Project description:Conventional mammography can suffer from poor contrast between healthy and cancerous tissues due to the small difference in attenuation properties. Coherent scatter slot scan imaging is an imaging technique which provides additional information and is compatible with conventional mammography. A Monte Carlo simulation of coherent scatter slot scan imaging was performed to assess its performance and provide system optimization. Coherent scatter could be exploited using a system similar to conventional slot scan mammography system with antiscatter grids tilted at the characteristic angle of cancerous tissues. System optimization was performed across several parameters, including source voltage, tilt angle, grid distances, grid ratio, and shielding geometry. The simulated carcinomas were detectable for tumors as small as 5 mm in diameter, so coherent scatter analysis using a wide-slot setup could be promising as an enhancement for screening mammography. Employing coherent scatter information simultaneously with conventional mammography could yield a conventional high spatial resolution image with additional coherent scatter information.
| S-EPMC4999523 | biostudies-other
Project description:UnlabelledBackgroundCost-effective production of lignocellulosic biofuels remains a major financial and technical challenge at the industrial scale. A critical tool in biofuels process development is the techno-economic (TE) model, which calculates biofuel production costs using a process model and an economic model. The process model solves mass and energy balances for each unit, and the economic model estimates capital and operating costs from the process model based on economic assumptions. The process model inputs include experimental data on the feedstock composition and intermediate product yields for each unit. These experimental yield data are calculated from primary measurements. Uncertainty in these primary measurements is propagated to the calculated yields, to the process model, and ultimately to the economic model. Thus, outputs of the TE model have a minimum uncertainty associated with the uncertainty in the primary measurements.ResultsWe calculate the uncertainty in the Minimum Ethanol Selling Price (MESP) estimate for lignocellulosic ethanol production via a biochemical conversion process: dilute sulfuric acid pretreatment of corn stover followed by enzymatic hydrolysis and co-fermentation of the resulting sugars to ethanol. We perform a sensitivity analysis on the TE model and identify the feedstock composition and conversion yields from three unit operations (xylose from pretreatment, glucose from enzymatic hydrolysis, and ethanol from fermentation) as the most important variables. The uncertainty in the pretreatment xylose yield arises from multiple measurements, whereas the glucose and ethanol yields from enzymatic hydrolysis and fermentation, respectively, are dominated by a single measurement: the fraction of insoluble solids (fIS) in the biomass slurries.ConclusionsWe calculate a $0.15/gal uncertainty in MESP from the TE model due to uncertainties in primary measurements. This result sets a lower bound on the error bars of the TE model predictions. This analysis highlights the primary measurements that merit further development to reduce the uncertainty associated with their use in TE models. While we develop and apply this mathematical framework to a specific biorefinery scenario here, this analysis can be readily adapted to other types of biorefining processes and provides a general framework for propagating uncertainty due to analytical measurements through a TE model.
| S-EPMC3503575 | biostudies-literature
Project description:Traditional multiple-group confirmatory factor analysis (multiple-group CFA) is usually criticized for having too restrictive model assumption, namely the scalar measurement invariance. The new multiple-group analysis methodology, alignment, has become an effective alternative. The alignment evaluates measurement invariance and more importantly, permits factor mean comparisons without requiring scalar invariance which is usually required in traditional multiple-group CFA. Some simulation studies and empirical studies have investigated the applicability of alignment under different conditions, but some areas remain unexplored. Based on the simulation studies of Asparouhov and Muthén and of Flake and McCoach, this current simulation study is broken into two sections. The first study investigates the minimal group sizes required for alignment in three-factor models. The second study compares the performance of multiple-group CFA, multiple-group exploratory structural equation model (multiple-group ESEM), and alignment by including different proportions and magnitudes of cross-loadings in the models. Study 1 shows that when the model has no noninvariant parameters, the alignment requires relatively lower group sizes. Explicitly, the minimal group size required for alignment was 250 when the amount of groups was three, the minimal group size was 150 when the amount of groups was nine, and 200 when the amount of groups was 15. When there are noninvariant parameters in the model and the amount of groups is low, a group size of 350 is a safe rule of thumb. When there are noninvariant parameters in the model and the amount of groups is high, a group size of 250 is required for trustworthy results. The magnitude of noninvariance and the noninvariance rate do not affect the minimal group size required for alignment. Study 2 shows that multiple-group CFA provides accurate factor mean estimates when each factor had 20% factor loading (1 factor loading) with small-sized cross-loading. Multiple-group ESEM provides accurate factor mean estimates when the magnitude of cross-loading is small or when each factor had 20% factor loading (1 factor loading) with medium-sized cross-loading. Alignment provides accurate factor mean estimates when there are only small-sized cross-loadings in the model. The parameter estimates, coverage rates and ratios of average standard error to standard deviation for each methodology are not influenced by the amount of groups. Recommendations are concluded for using multiple-group CFA, multiple-group ESEM, traditional alignment and aligned ESEM (AESEM) based on the results. Multiple-group CFA is more suitable for use when scalar invariance is established. Multiple-group ESEM works best when there are small-sized or only a few medium-sized cross-loadings in the model. Traditional alignment allows for small-sized cross-loadings and a few noninvariant parameters in the model. AESEM integrates the advantages of alignment and ESEM, can provide accurate estimates when noninvariant parameters and cross-loadings both exist in the model. Compared to multiple-group CFA, multiple-group ESEM, the alignment methodology performs well in more situations.
| S-EPMC9263979 | biostudies-literature
Project description:A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys. 2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD-MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD-MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems.
| S-EPMC4535364 | biostudies-literature
Project description:The objective of this study was to separately describe the fitting uncertainty and the variability of individual cell in bacterial survival kinetics during isothermal and non-isothermal thermal processing. The model describing bacterial survival behavior and its uncertainties and variabilities during non-isothermal inactivation was developed from survival kinetic data for Bacillus simplex spores under fifteen isothermal conditions. The fitting uncertainties in the parameters used in the primary Weibull model was described by using the bootstrap method. The variability of individual cells in thermotolerance and the true randomness in the number of dead cells were described by using the Markov chain Monte Carlo (MCMC) method. A second-order Monte Carlo (2DMC) model was developed by combining both the uncertainties and variabilities. The 2DMC model was compared with reduction behavior under three non-isothermal profiles for model validation. The bacterial death estimations were validated using experimentally observed surviving bacterial count data. The fitting uncertainties in the primary Weibull model parameters, the individual thermotolerance heterogeneity, and the true randomness of inactivated spore counts were successfully described under all the iso-thermal conditions. Furthermore, the 2DMC model successfully described the variances in the surviving bacterial counts during thermal inactivation for all three non-isothermal profiles. As a template for risk-based process designs, the proposed 2DMC simulation approach, which considers both uncertainty and variability, can facilitate the selection of appropriate thermal processing conditions ensuring both food safety and quality.
| S-EPMC7248279 | biostudies-literature
Project description:BACKGROUND: In the biological sciences the TCID50 (median tissue culture infective dose) assay is often used to determine the strength of a virus. METHODS: When the so-called Spearman-Kaerber calculation is used, the ratio between the pfu (the number of plaque forming units, the effective number of virus particles) and the TCID50, theoretically approaches a simple function of Eulers constant. Further, the standard deviation of the logarithm of the TCID50 approaches a simple function of the dilution factor and the number of wells used for determining the ratios in the assay. However, these theoretical calculations assume that the dilutions of the assay are independent, and in practice this is not completely correct. The assay was simulated using Monte Carlo techniques. RESULTS: Our simulation studies show that the theoretical results actually hold true for practical implementations of the assay. Furthermore, the simulation studies show that the distribution of the (the log of) TCID50, although discrete in nature, has a close relationship to the normal distribution. CONCLUSION: The pfu is proportional to the TCID50 titre with a factor of about 0.56 when using the Spearman-Kaerber calculation method. The normal distribution can be used for statistical inferences and ANOVA on the (the log of) TCID50 values is meaningful with group sizes of 5 and above.
| S-EPMC3331834 | biostudies-other