Optimizing malaria vector control in the Greater Mekong Subregion: a systematic review and mathematical modelling study to identify desirable intervention characteristics

BACKGROUND

In the Greater Mekong Subregion (GMS), new vector-control tools are needed to target mosquitoes that bite outside during the daytime and night-time to advance malaria elimination.

METHODS

We conducted systematic literature searches to generate a bionomic dataset of the main malaria vectors in the GMS, including human blood index (HBI), parity proportion, sac proportion (proportion with uncontracted ovary sacs, indicating the amount of time until they returned to host seeking after oviposition) and the resting period duration. We then performed global sensitivity analyses to assess the influence of bionomics and intervention characteristics on vectorial capacity.

RESULTS

Our review showed that Anopheles minimus, An. sinensis, An. maculatus and An. sundaicus display opportunistic blood-feeding behaviour, while An. dirus is more anthropophilic. Multivariate regression analysis indicated that environmental, climatic and sampling factors influence the proportion of parous mosquitoes, and resting duration varies seasonally. Sensitivity analysis highlighted HBI and parity proportion as the most influential bionomic parameters, followed by resting duration. Killing before feeding is always a desirable characteristic across all settings in the GMS. Disarming is also a desirable characteristic in settings with a low HBI. Repelling is only an effective strategy in settings with a low HBI and low parity proportion. Killing after feeding is only a desirable characteristic if the HBI and parity proportions in the setting are high.

CONCLUSIONS

Although in general adopting tools that kill before feeding would have the largest community-level effect on reducing outdoor transmission, other modes of action can be effective. Current tools in development which target outdoor biting mosquitoes should be implemented in different settings dependent on their characteristics.

Tool for fast assessment of stormwater flood volumes for urban catchment: A machine learning approach

Specific flood volume is an important criterion for evaluating the performance of sewer networks. Currently, mechanistic models - MCMs (e.g., SWMM) are usually used for its prediction, but they require the collection of detailed information about the characteristics of the catchment and sewer network, which can be difficult to obtain, and the process of model calibration is a complex task. This paper presents a methodology for developing simulators to predict specific flood volume using machine learning methods (DNN - Deep Neural Network, GAM - Generalized Additive Model). The results of Sobol index calculations using the GSA method were used to select the ML model as an alternative to the MCM model. It was shown that the DNN model can be used for flood prediction, for which high agreement was obtained between the results of GSA calculations for rainfall data, catchment and sewer network characteristics, and calibrated SWMM parameters describing land use and sewer retention. Regression relationships (polynomials and exponential functions) were determined between Sobol indices (retention depth of impervious area, correction factor of impervious area, Manning's roughness coefficient of sewers) and sewer network characteristics (unit density of sewers, retention factor - the downstream and upstream of retention ratio) obtaining R2 = 0. 55-0.78. The feasibility of predicting sewer network flooding and modernization with the DNN model using a limited range of input data compared to the SWMM was shown. The developed model can be applied to the management of urban catchments with limited access to data and at the stage of urban planning.

Fracture behaviour assessment of high-performance fibre-reinforced concrete at high strain rates using interpretable modelling approaches

High-performance fibre-reinforced concrete (HPFRC), a type of cementitious composite material known for its exceptional mechanical performance, has widespread applications in structures exposed to severe dynamic loading conditions. However, understanding nonlinear HPFRC fracture behaviour, particularly under high strain rates, remains challenging given the complexities of assessment procedures and cost-intensive nature of experiments. This study presents an interpretable framework for modelling and analysing HPFRC fracture strength at high strain rates. A wide range of machine learning methods, including ensemble techniques, were employed to capture multivariate effects of eight essential input features (e.g., mortar compressive strength, fibre physical and mechanical properties, cross-sectional area, and strain rate) on fracture strength response. To assess the derived models, a novel evaluation procedure was proposed involving a data-based analysis, employing established metrics (i.e., coefficient of determination, root mean squared error, and mean absolute error via K-fold cross-validation) and a domain experts-involved evaluation utilising global sensitivity analysis to discern first-order and higher-order interactions among input factors. The proposed approach efficiently yielded both quantitative and qualitative insights into crucial input factors governing HPFRC fracture strength with limited experimental data. The obtained findings highlight the significance of multivariate effects, such as the interaction between strain rate and fibre tensile strength, and between fibre volume and fibre diameter, on fracture behaviour. The proposed interpretable framework aims to provide a powerful tool for proactive material failure analysis by understanding fracture behaviour and identifying potential weak and strong interactions among input factors of HPFRC-based samples. Moreover, the utilisation of the proposed approach enables researchers and civil engineers to efficiently focus on the most critical input parameters during the early design stage and ensuring the structural integrity and safety of HPFRC-based constructions.

Assessing runoff control of low impact development in Hong Kong's dense community with reliable SWMM setup and calibration

Low impact development (LID) is a sustainable practice to managing urban runoff. However, its effectiveness in densely populated areas with intense rainfall, such as Hong Kong, remains unclear due to limited studies with similar climate conditions and urban patterns. The highly mixed land use and complicated drainage network present challenges for preparing a Storm Water Management Model (SWMM). This study proposed a reliable framework for setting up and calibrating SWMM by integrating multiple automated tools to address these issues. With a validated SWMM, we examined LID's effects on runoff control in a densely built catchment of Hong Kong. A designed full-scale LID implementation can reduce total and peak runoffs by around 35-45% for 2, 10 and 50-year return rainfalls. However, LID alone may not be adequate to handle the runoff in densely built areas of Hong Kong. As the rainfall return period increases, total runoff reduction increases, but peak runoff reduction remains close. Percentages of reduction in total and peak runoffs decline. The marginal control diminishes for total runoff while remaining constant for peak runoff when increasing the extent of LID implementation. In addition, the study identifies the crucial design parameters of LID facilities using global sensitivity analysis. Overall, our study contributes to accelerating the reliable application of SWMM and deepening the understanding of the effectiveness of LID in ensuring water security in densely built urban communities located near the humid-tropical climate zone, such as Hong Kong.

Probabilistic assessment of failure of infiltration structures under model and parametric uncertainty

We focus on the quantification of the probability of failure (PF) of an infiltration structure, of the kind that is typically employed for the implementation of low impact development strategies in urban settings. Our approach embeds various sources of uncertainty. These include (a) the mathematical models rendering key hydrological traits of the system and the ensuing model parametrization as well as (b) design variables related to the drainage structure. As such, we leverage on a rigorous multi-model Global Sensitivity Analysis framework. We consider a collection of commonly used alternative models to represent our knowledge about the conceptualization of the system functioning. Each model is characterized by a set of uncertain parameters. As an original aspect, the sensitivity metrics we consider are related to a single- and a multi-model context. The former provides information about the relative importance that model parameters conditional to the choice of a given model can have on PF. The latter yields the importance that the selection of a given model has on PF and enables one to consider at the same time all of the alternative models analyzed. We demonstrate our approach through an exemplary application focused on the preliminary design phase of infiltration structures serving a region in the northern part of Italy. Results stemming from a multi-model context suggest that the contribution arising from the adoption of a given model is key to the quantification of the degree of importance associated with each uncertain parameter.

An integrated modelling approach for targeted degradation: insights on optimization, data requirements and PKPD predictions from semi- or fully-mechanistic models and exact steady state solutions

The value of an integrated mathematical modelling approach for protein degraders which combines the benefits of traditional turnover models and fully mechanistic models is presented. Firstly, we show how exact solutions of the mechanistic models of monovalent and bivalent degraders can provide insight on the role of each system parameter in driving the pharmacological response. We show how on/off binding rates and degradation rates are related to potency and maximal effect of monovalent degraders, and how such relationship can be used to suggest a compound optimization strategy. Even convoluted exact steady state solutions for bivalent degraders provide insight on the type of observations required to ensure the predictive capacity of a mechanistic approach. Specifically for PROTACs, the structure of the exact steady state solution suggests that the total remaining target at steady state, which is easily accessible experimentally, is insufficient to reconstruct the state of the whole system at equilibrium and observations on different species (such as binary/ternary complexes) are necessary. Secondly, global sensitivity analysis of fully mechanistic models for PROTACs suggests that both target and ligase baselines (actually, their ratio) are the major sources of variability in the response of non-cooperative systems, which speaks to the importance of characterizing their distribution in the target patient population. Finally, we propose a pragmatic modelling approach which incorporates the insights generated with fully mechanistic models into simpler turnover models to improve their predictive ability, hence enabling acceleration of drug discovery programs and increased probability of success in the clinic.

A two-stages global sensitivity analysis by using the δ sensitivity index in presence of correlated inputs: application on a tumor growth inhibition model based on the dynamic energy budget theory

Global sensitivity analysis (GSA) evaluates the impact of variability and/or uncertainty of the model parameters on given model outputs. GSA is useful for assessing the quality of Pharmacometric model inference. Indeed, model parameters can be affected by high (estimation) uncertainty due to the sparsity of data. Independence between model parameters is a common assumption of GSA methods. However, ignoring (known) correlations between parameters may alter model predictions and, then, GSA results. To address this issue, a novel two-stages GSA technique based on the δ index, which is well-defined also in presence of correlated parameters, is here proposed. In the first step, statistical dependencies are neglected to identify parameters exerting causal effects. Correlations are introduced in the second step to consider the real distribution of the model output and investigate also the 'indirect' effects due to the correlation structure. The proposed two-stages GSA strategy was applied, as case study, to a preclinical tumor-in-host-growth inhibition model based on the Dynamic Energy Budget theory. The aim is to evaluate the impact of the model parameter estimate uncertainty (including correlations) on key model-derived metrics: the drug threshold concentration for tumor eradication, the tumor volume doubling time and a new index evaluating the drug efficacy-toxicity trade-off. This approach allowed to rank parameters according to their impact on the output, discerning whether a parameter mainly exerts a causal or 'indirect' effect. Thus, it was possible to identify uncertainties that should be necessarily reduced to obtain robust predictions for the outputs of interest.

A new probabilistic assessment process for human health risk (HHR) in groundwater with extensive fluoride and nitrate optimized by non parametric estimation method

Excessive amounts of fluoride (F-) and nitrate (NO3-) in groundwater pose a significant threat to human health. However, a quantitative approach to assessing the human health risks caused by these harmful substances is lacking. To optimize the probabilistic assessment process for human health risk (HHR), this study introduced kernel density estimation (KDE) into the stochastic simulation of F- and NO3- content in groundwater samples. The potential HHRs caused by F- and NO3- in Songyuan City were summarized by combining the probabilistic and deterministic assessments. This study found that the concentrations of F- and NO3- did not follow common probability density functions (PDFs), but the KDE method passed the Kolmogorov-Smirnov test with the critical value of 0.067 and 0.062, showing high fitting accuracy. Monte Carlo simulation indicated that the probability of NO3- for children and adult exceeding the standard is 21.95% and 15.14%, respectively, which is comparable with the results of the deterministic assessment, but the probabilistic assessment emphasized lower probability of HHRs in children caused by excess F-(4.14%). Global sensitivity analysis revealed that excessive NO3- in groundwater has the highest sensitivity of the HHR (>0.1), followed by other factors representing water use habits (>0.01). This study presents a refined probabilistic assessment method for HHR and provides a scientific reference for understanding the state of groundwater environments.

Environmental vulnerability assessment of the Doce River basin, southeastern Brazil

Environmental vulnerability is an important tool to understand the natural and anthropogenic impacts associated with the susceptibility to environmental damage. This study aims to assess the environmental vulnerability of the Doce River basin in Brazil through Multicriteria Decision Analysis based on Geographic Information Systems (GIS-MCDA). Natural factors (slope, elevation, relief dissection, rainfall, pedology, and geology) and anthropogenic factors (distance from urban centers, roads, mining dams, and land use) were used to determine the environmental vulnerability index (EVI). The EVI was classified into five classes, identifying associated land uses. Vulnerability was verified in water resource management units (UGRHs) and municipalities using hot spot analysis. The study employed the water quality index (WQI) to assess the EVI and global sensitivity analysis (GSA) to evaluate the model input parameters that most influence the basin's environmental vulnerability. The results showed that the regions near the middle Doce River were considered environmentally more vulnerable, especially the UGRHs Guandu, Manhuaçu, and Caratinga; and 35.9% of the basin has high and very high vulnerabilities. Hot spot analysis identified regions with low EVI values (cold spot) in the north and northwest, while areas with high values (hot spot) were concentrated mainly in the middle Doce region. Water monitoring stations with the worst WQI values were found in the most environmentally vulnerable areas. The GSA determined that land use and slope were the primary factors influencing the model's response. The results of this study provide valuable information for supporting environmental planning in the Doce River basin.

Learning-based sensitivity analysis and feedback design for drug delivery of mixed therapy of cancer in the presence of high model uncertainties

In this paper, a methodology is proposed that enables to analyze the sensitivity of the outcome of a therapy to unavoidable high dispersion of the patient specific parameters on one hand and to the choice of the parameters that define the drug delivery feedback strategy on the other hand. More precisely, a method is given that enables to extract and rank the most influent parameters that determine the probability of success/failure of a given feedback therapy for a given set of initial conditions over a cloud of realizations of uncertainties. Moreover predictors of the expectations of the amounts of drugs being used can also be derived. This enables to design an efficient stochastic optimization framework that guarantees safe contraction of the tumor while minimizing a weighted sum of the quantities of the different drugs being used. The framework is illustrated and validated using the example of a mixed therapy of cancer involving three combined drugs namely: a chemotherapy drug, an immunology vaccine and an immunotherapy drug. Finally, in this specific case, it is shown that dash-boards can be built in the 2D-space of the most influent state components that summarize the outcomes' probabilities and the associated drug usage as iso-values curves in the reduced state space.

Exploring how ecological and epidemiological processes shape multi-host disease dynamics using global sensitivity analysis

We use global sensitivity analysis (specifically, Partial Rank Correlation Coefficients) to explore the roles of ecological and epidemiological processes in shaping the temporal dynamics of a parameterized SIR-type model of two host species and an environmentally transmitted pathogen. We compute the sensitivities of disease prevalence in each host species to model parameters. Sensitivity rankings are calculated, interpreted biologically, and contrasted for cases where the pathogen is introduced into a disease-free community and cases where a second host species is introduced into an endemic single-host community. In some cases the magnitudes and dynamics of the sensitivities can be predicted only by knowing the host species' characteristics (i.e., their competitive abilities and disease competence) whereas in other cases they can be predicted by factors independent of the species' characteristics (specifically, intraspecific versus interspecific processes or a species' roles of invader versus resident). For example, when a pathogen is initially introduced into a disease-free community, disease prevalence in both hosts is more sensitive to the burst size of the first host than the second host. In comparison, disease prevalence in each host is more sensitive to its own infection rate than the infection rate of the other host species. In total, this study illustrates that global sensitivity analysis can provide useful insight into how ecological and epidemiological processes shape disease dynamics and how those effects vary across time and system conditions. Our results show that sensitivity analysis can provide quantification and direction when exploring biological hypotheses.

Framework for global sensitivity analysis in a complex 1D-2D coupled hydrodynamic model: Highlighting its importance on flood management over large data-scarce regions

Sensitivity analysis determines how perturbation or variation in the values of an independent variable affects a particular dependent variable. The present study attempts to comprehend the sensitivity of the static input parameters on the accuracy of the outputs in a hydrodynamic flood model, which subsequently improves the model accuracy. Hydrodynamic flood modeling is computationally strenuous and data-intensive. Moreover, the accuracy of the flood model outputs is extremely sensitive to the quality of hydrologic and hydraulic inputs, along with a set of static parameters that are traditionally assumed and primarily used for calibration. Therefore, we focus on developing a framework for global sensitivity analysis (GSA) of static input parameters in a 1D-2D coupled hydrodynamic flood modeling system. A set of numerical experiments is conducted by perturbing various combinations of input parameters from their standard (or observed) values to generate flow hydrographs. Nonparametric probability density functions (PDFs) of the river discharge at different locations are compared to calculate the Kullback-Leibler (KL) entropy or KL-divergence, which is used to quantify the sensitivity of the input parameters. We demonstrated the proposed framework on a highly flood-prone rural catchment of the Shilabati River in West Bengal, India, and infer that the sensitivity of the static input parameters is highly dynamic, and their importance varies spatially from the upstream to the downstream of the river. However, Manning's n values of the channel and the banks are significantly sensitive irrespective of the location in the river reach. We suggest that any flood modeling exercise should accompany a GSA, which sets a guideline for the modelers to prioritize the set of sensitive static input parameters during data monitoring, collection, and retrieval. This study is the first attempt at a GSA in a 1D-2D coupled hydrodynamic flood modeling system, whose importance cannot be over-emphasized in any flood modeling platform. The proposed novel framework is generic and can be implemented prior to flood risk analyses for any floodplain management exercise. All free and commercially-available flood models can incorporate the proposed framework for a GSA as an extension toolbox.

Tumour growth: An approach to calibrate parameters of a multiphase porous media model based on in vitro observations of Neuroblastoma spheroid growth in a hydrogel microenvironment

To unravel processes that lead to the growth of solid tumours, it is necessary to link knowledge of cancer biology with the physical properties of the tumour and its interaction with the surrounding microenvironment. Our understanding of the underlying mechanisms is however still imprecise. We therefore developed computational physics-based models, which incorporate the interaction of the tumour with its surroundings based on the theory of porous media. However, the experimental validation of such models represents a challenge to its clinical use as a prognostic tool. This study combines a physics-based model with in vitro experiments based on microfluidic devices used to mimic a three-dimensional tumour microenvironment. By conducting a global sensitivity analysis, we identify the most influential input parameters and infer their posterior distribution based on Bayesian calibration. The resulting probability density is in agreement with the scattering of the experimental data and thus validates the proposed workflow. This study demonstrates the huge challenges associated with determining precise parameters with usually only limited data for such complex processes and models, but also demonstrates in general how to indirectly characterise the mechanical properties of neuroblastoma spheroids that cannot feasibly be measured experimentally.

A mechanistic approach to include climate change and unplanned urban sprawl in landslide susceptibility maps

Empirical evidence shows that climate, deforestation and informal housing (i.e. unregulated construction practices typical of fast-growing developing countries) can increase landslide occurrence. However, these environmental changes have not been considered jointly and in a dynamic way in regional or national landslide susceptibility assessments. This gap might be due to a lack of models that can represent large areas (>100km²) in a computationally efficient way, while simultaneously considering the effect of rainfall infiltration, vegetation and housing. We therefore suggest a new method that uses a hillslope-scale mechanistic model to generate regional susceptibility maps under changing climate and informal urbanisation, which also accounts for existing uncertainties. An application in the Caribbean shows that the landslide susceptibility estimated with the new method and associated with a past rainfall-intensive hurricane identifies ~67.5 % of the landslides observed after that event. We subsequently demonstrate that the hypothetical expansion of informal housing (including deforestation) increases landslide susceptibility more (+20 %) than intensified rainstorms due to climate change (+6 %). However, their combined effect leads to a much greater landslide occurrence (up to +40 %) than if the two drivers were considered independently. Results demonstrate the importance of including both land cover and climate change in landslide susceptibility assessments. Furthermore, by modelling mechanistically the overlooked dynamics between urban growth and climate change, our methodology can provide quantitative information of the main landslide drivers (e.g. quantifying the relative impact of deforestation vs informal urbanisation) and locations where these drivers are or might become most detrimental for slope stability. Such information is often missing in data-scarce developing countries but is key for supporting national long-term environmental planning, for targeting financial efforts, as well as for fostering national or international investments for landslide mitigation.

Morphological parameters affecting false lumen thrombosis following type B aortic dissection: a systematic study based on simulations of idealized models

Type B aortic dissection (TBAD) carries a high risk of complications, particularly with a partially thrombosed or patent false lumen (FL). Therefore, uncovering the risk factors leading to FL thrombosis is crucial to identify high-risk patients. Although studies have shown that morphological parameters of the dissected aorta are related to FL thrombosis, often conflicting results have been reported. We show that recent models of thrombus evolution in combination with sensitivity analysis methods can provide valuable insights into how combinations of morphological parameters affect the prospect of FL thrombosis. Based on clinical data, an idealized geometry of a TBAD is generated and parameterized. After implementing the thrombus model in computational fluid dynamics simulations, a global sensitivity analysis for selected morphological parameters is performed. We then introduce dimensionless morphological parameters to scale the results to individual patients. The sensitivity analysis demonstrates that the most sensitive parameters influencing FL thrombosis are the FL diameter and the size and location of intimal tears. A higher risk of partial thrombosis is observed when the FL diameter is larger than the true lumen diameter. Reducing the ratio of the distal to proximal tear size increases the risk of FL patency. In summary, these parameters play a dominant role in classifying morphologies into patent, partially thrombosed, and fully thrombosed FL. In this study, we point out the predictive role of morphological parameters for FL thrombosis in TBAD and show that the results are in good agreement with available clinical studies.

Modeling and Global Sensitivity Analysis of Strategies to Mitigate Covid-19 Transmission on a Structured College Campus

In response to the COVID-19 pandemic, many higher educational institutions moved their courses on-line in hopes of slowing disease spread. The advent of multiple highly-effective vaccines offers the promise of a return to "normal" in-person operations, but it is not clear if-or for how long-campuses should employ non-pharmaceutical interventions such as requiring masks or capping the size of in-person courses. In this study, we develop and fine-tune a model of COVID-19 spread to UC Merced's student and faculty population. We perform a global sensitivity analysis to consider how both pharmaceutical and non-pharmaceutical interventions impact disease spread. Our work reveals that vaccines alone may not be sufficient to eradicate disease dynamics and that significant contact with an infectious surrounding community will maintain infections on-campus. Our work provides a foundation for higher-education planning allowing campuses to balance the benefits of in-person instruction with the ability to quarantine/isolate infectious individuals.

Global sensitivity analysis in epidemiological modeling

Operations researchers worldwide rely extensively on quantitative simulations to model alternative aspects of the COVID-19 pandemic. Proper uncertainty quantification and sensitivity analysis are fundamental to enrich the modeling process and communicate correctly informed insights to decision-makers. We develop a methodology to obtain insights on key uncertainty drivers, trend analysis and interaction quantification through an innovative combination of probabilistic sensitivity techniques and machine learning tools. We illustrate the approach by applying it to a representative of the family of susceptible-infectious-recovered (SIR) models recently used in the context of the COVID-19 pandemic. We focus on data of the early pandemic progression in Italy and the United States (the U.S.). We perform the analysis for both cases of correlated and uncorrelated inputs. Results show that quarantine rate and intervention time are the key uncertainty drivers, have opposite effects on the number of total infected individuals and are involved in the most relevant interactions.

Prioritizing vaccination based on analysis of community networks

Many countries that had early access to COVID-19 vaccines implemented vaccination strategies that prioritized health care workers and the elderly. As barriers to access eased, vaccine prioritization strategies have been relaxed. However, these strategies are still an important tool for decision makers to manage new variants, plan for future booster shots, or stage mass vaccinations. This paper explores the impact of vaccine prioritization strategies using networks that represent communities with different demographics and connectivity. The impact of vaccination is compared to non-medical intervention to reduce transmission. Several sources of uncertainty are considered, including vaccine willingness and mask effectiveness. This paper finds that while prioritization strategies can have a large impact on reducing deaths and peak hospitalization, selecting the best strategy depends on community characteristics and the desired objective. Additionally, in some cases random vaccination performs as well as more targeted prioritization strategies. Understanding these trade-offs is important when planning vaccine distribution.

Hyperspectral response of agronomic variables to background optical variability: Results of a numerical experiment

Understanding how biophysical and biochemical variables contribute to the spectral characteristics of vegetation canopies is critical for their monitoring. Quantifying these contributions, however, remains difficult due to extraneous factors such as the spectral variability of canopy background materials, including soil/crop-residue moisture, soil-type, and non-photosynthetic vegetation (NPV). This study focused on exploring the spectral response of two important agronomic variables (1) leaf chlorophyll content (Cab ) and (2) leaf area index (LAI) under various canopy backgrounds through a global sensitivity analysis of wheat-like canopy spectra simulated using the physically-based PROSAIL radiative transfer model. Our results reveal the following general findings: (1) the contribution of each agronomic variable to the simulated canopy spectral signature varies considerably with respect to the background optical properties; (2) the influence of the soil-type and NPV on the spectral response of canopy to Cab and LAI is more significant than that caused by soil/crop-residue moisture; (3) spectral bands at 560 and 704 nm remain sensitive to Cab while being least affected by the impacts of variations in the NPV, soil-type and moisture; (4) the near-infrared (NIR) spectral bands exhibit higher sensitivity to LAI and lower background effects only in the cases of soil/crop-residue moisture but are relatively strongly affected by soil-type and NPV. Comparative analysis of the correlations of twelve widely used vegetation indices with agronomic variables indicates that LICI (LAI-insensitive chlorophyll index) and Macc01 (Maccioni index) are more effective in estimating Cab , while OSAVI (optimized soil adjusted vegetation index) and MCARI2 (modified chlorophyll absorption ratio index 2) are better LAI predictors under the simulated background variability. Overall, our results highlight that background reflectance variability introduces considerable differences in the agronomic variables' spectral response, leading to inconsistencies in the VI- Cab /-LAI relationship. Further studies should integrate these results of spectral responsivity to develop trait-specific hyperspectral inversion models.

Global sensitivity analysis of VISSIM parameters for project-level traffic emissions: a case study at a signalized intersection

Combining traffic micro-simulation models and emission models is a primary method to estimate traffic emissions. However, there has been limited research on the impact of traffic micro-simulation model parameters on simulator outputs, which are critical to emissions calculations. Based on combining VISSIM and MOVES, this study uses the Morris and Sobol methods to explore the impact of parameters in VISSIM on operating mode distribution and travel time distribution. Taking an urban signal control intersection with three traffic scenarios in Chengdu, China as an example, this study verifies the methods' feasibility. Apart from these parameters, which have been proved to be necessary calibration parameters, including the desired speed distribution, the desired acceleration function, and the desired deceleration function, an additional 24 parameters related to simulation setting and driving behaviour models are selected as the initial parameters. The number of interaction objects, maximum look-ahead distance, average standstill distance, additive part of safety distance, and safety distance reduction factor close to a stop line, are considered to be the important parameters for this case study. The impact of these five parameters on the bins of operating mode distribution and travel time distribution are further analyzed with One-at-a-time, and these parameters are compared with those reported in previous studies. It is concluded that the important parameters selected in this study are reasonable and can support the calibration of VISSIM parameters for this case's traffic emissions.

Where is the greatest potential for resource recovery in wastewater treatment plants?

The restorative and regenerative ability of the circular economy has led to the rapid growth of this concept over the past decade, as it facilitates the broadly adopted principles of sustainable development and beyond, through restorative and regenerative actions. The water sector is poised to benefit from this transition, due to its intrinsic circularity and the resources it handles, predominantly found in wastewater, that are valuable and critical. Currently, the vast range of resource recovery technologies coupled with few industrial examples hinder strategic decision making. Resource recovery on a regional scale improves market share and mitigates investment risk, therefore, a structured approach has been developed for the selection of priority technologies to act as a guide for strategic planning. A representative UK wastewater model acts as the baseline, with multi-criteria analysis used to select resources and create an enhanced resource recovery scenario. It was found that implementing the recovery of 5 'priority resources' (and technology pathways) increased nitrogen and phosphorus recovery by 68% and 71%, respectively. Lastly, the need for a cross-cutting approach for the holistic assessment of circular solutions is discussed.

Sensitivity analysis and inverse uncertainty quantification for the left ventricular passive mechanics

Personalized computational cardiac models are considered to be a unique and powerful tool in modern cardiology, integrating the knowledge of physiology, pathology and fundamental laws of mechanics in one framework. They have the potential to improve risk prediction in cardiac patients and assist in the development of new treatments. However, in order to use these models for clinical decision support, it is important that both the impact of model parameter perturbations on the predicted quantities of interest as well as the uncertainty of parameter estimation are properly quantified, where the first task is a priori in nature (meaning independent of any specific clinical data), while the second task is carried out a posteriori (meaning after specific clinical data have been obtained). The present study addresses these challenges for a widely used constitutive law of passive myocardium (the Holzapfel-Ogden model), using global sensitivity analysis (SA) to address the first challenge, and inverse-uncertainty quantification (I-UQ) for the second challenge. The SA is carried out on a range of different input parameters to a left ventricle (LV) model, making use of computationally efficient Gaussian process (GP) surrogate models in place of the numerical forward simulator. The results of the SA are then used to inform a low-order reparametrization of the constitutive law for passive myocardium under consideration. The quality of this parameterization in the context of an inverse problem having observed noisy experimental data is then quantified with an I-UQ study, which again makes use of GP surrogate models. The I-UQ is carried out in a Bayesian manner using Markov Chain Monte Carlo, which allows for full uncertainty quantification of the material parameter estimates. Our study reveals insights into the relation between SA and I-UQ, elucidates the dependence of parameter sensitivity and estimation uncertainty on external factors, like LV cavity pressure, and sheds new light on cardio-mechanic model formulation, with particular focus on the Holzapfel-Ogden myocardial model.

Global sensitivity analysis in physiologically-based pharmacokinetic/pharmacodynamic models of inhaled and opioids anesthetics and its application to generate virtual populations

The integration between physiologically-based pharmacokinetics (PBPK) models and pharmacodynamics (PD) models makes it possible to describe the absorption, distribution, metabolism and excretion processes of drugs, together with the concentration-response relationship, being a fundamental framework with wide applications in pharmacology. Nevertheless, the enormous complexity of PBPK models and the large number of parameters that define them leads to the need to study and understand how the uncertainty of the parameters affects the variability of the models output. To study this issue, this paper proposes a global sensitivity analysis (GSA) to identify the parameters that have the greatest influence on the response of the model. It has been selected as study cases the PBPK models of an inhaled anesthetic and an analgesic, along with two PD interaction models that describe two relevant clinical effects, hypnosis and analgesia during general anesthesia. The subset of the most relevant parameters found adequately with the GSA method has been optimized for the generation of a virtual population that represents the theoretical output variability of various model responses. The generated virtual population has the potential to be used for the design, development and evaluation of physiological closed-loop control systems.

Uncertainty analysis of ecosystem services and implications for environmental management - An experiment in the Heihe River Basin, China

Integrating the economic values of ecosystem services provided by different land uses into decision analysis is critical to achieving effective environmental management in endorheic basins. However, policymaking often ignores the uncertainty related to the variability of parameters in ecosystem service values. To this end, we identified sensitive parameters in the ecosystem service values under four land uses using the global sensitivity analysis method and quantified the potential monetary outcomes based on the Monte Carlo method. The results indicated that only a few sensitive parameters, such as water yield (Q_i) and treatment costs per unit of nitrogen (Cost_N), were the primary sources of uncertainty. Therefore, we suggest that improving the precision of sensitive parameters is essential for reducing uncertainty in the total ecosystem service value. Additionally, the overall monetary outcomes for cropland exhibited negative values and had higher risk and lower benefits than those for forest from the standpoint of ecosystem services. In addition, the nonmarketed service of landscape aesthetic made the monetary outcomes of water bodies higher than those of cropland, yet the value of landscape aesthetic was highly uncertain. Therefore, efforts should be made to improve total monetary outcomes by decreasing the negative values in food provisioning of cropland and the uncertainty in landscape aesthetic for water bodies. The sensitivity analysis and uncertainty analysis provide important guidelines for quantifying and reducing the related uncertainty and provide policy information for environmental management based on a comprehensive consideration of the potential ecosystem service values for various land uses.

A note on the effect of material uncertainty on acoustic source localization error in anisotropic plates

The uncertainty in material properties of an anisotropic plate may influence the acoustic source localization process undertaken for the plate. To study this effect of material uncertainty, the two moduli of elasticity of an orthotropic plate material are considered in this note as independent random variables and the propagation of this material uncertainty through the wave front shape-based acoustic source localization approach is investigated. Assuming lognormal probability distributions for the two random variables, several design points in lognormal spaces are picked using Latin Hypercube Sampling. Finite element analysis is performed for each design point to simulate the elastic wave propagation due to an acoustic event and wave front shape-based approach is applied to estimate the source location. The time-of-arrivals and source localization errors obtained for each design point are considered as separate response functions at that design point and regression kriging metamodels through the responses at the design points are constructed. Monte Carlo simulations are carried out using these metamodels to obtain the distribution parameters (i.e., ranges, means and standard deviations) of the time-of-arrivals and localization errors. A global sensitivity analysis is performed to estimate the effect of each random variable on the localization errors. It is observed that for lognormally distributed moduli of elasticity with same coefficients of variation, uncertainty in the modulus of elasticity in the major direction affects the source localization accuracy more compared to the uncertainty in the modulus of elasticity in the minor direction, particularly when the ellipse-based technique is used.

Implementation of supervised principal component analysis for global sensitivity analysis of models with correlated inputs

Global Sensitivity Analysis (GSA) plays a significant role in quantifying the tangible impact of model inputs on the uncertainty of response variable. As GSA results are strongly affected by correlated inputs, several studies have considered this issue, but most of them are computationally expensive, labor-intensive, and difficult to implement. Accordingly, this paper puts forward a novel regression-based strategy based on the Supervised Principal Component Analysis (SPCA), benefiting from the Reproducing Kernel Hilbert Space. Indeed, by conducting one kind of variance-based sensitivity analysis, a renowned method exclusively customized for models with orthogonal inputs, on SPCA regression, the impact of the correlation structure of input variables is considered. The ability of the suggested technique is evaluated with five test cases as well as three hydrologic and hydraulic models, and the results are compared with those obtained from the correlation ratio method; Taken as a benchmark solution, which is a robust but quite complicated approach in terms of programming. It is found that the proposed method satisfactorily identifies the sensitivity ordering of model inputs. Furthermore, it is proved in this study that the performance of the proposed approach is also supported by the total contribution index in the derived covariance decomposition equation. Moreover, the proposed method compared with the correlation ratio method, is found to be computationally efficient and easy to implement. Overall, the proposed scheme is appropriate for high dimensional, quite strong nonlinear or expensive models with correlated inputs, whose coefficient of determination between the original model and regression-based SPCA model is larger than 0.33.

Modelling botanical biofiltration of indoor air streams contaminated by volatile organic compounds

Botanical filtration is a biological-based treatment method suitable for removing hazardous volatile organic compounds (VOCs) from air streams, based on forcing an air flow through a porous substrate and foliage of a living botanical compartment. The pathways and removal mechanisms during VOC bioremediation have been largely investigated; however, their mathematical representation is well established only for the non-botanical components of the system. In this study, we evaluated the applicability of such a modelling scheme to systems which include a botanical compartment. We implemented a one-dimensional numerical model and performed a global sensitivity analysis to measure the input parameters influence on the transient and steady biofilter responses. We found that the most sensitive parameters on the transient-state behaviour were the mass transfer coefficient between gas and solid surfaces, and the fraction of solid surfaces covered by the biofilm; the steady-state response was primarily influenced by the biofilm specific surface area and the fraction of surfaces covered by the biofilm. We calibrated the identified set of parameters and successfully validated the model against data from a pilot-scale installation. The results showed that the application of the model to systems with a botanical compartment is feasible, although under a strict set of assumptions.

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

Neuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a variety of different software tools in the model building and analysis process. Here we focus on the scale of biochemical pathways, which is one of the main objects of study in systems biology. While systems biology is among the more standardized fields, conversion between different model formats and interoperability between various tools is still somewhat problematic. To offer our take on tackling these shortcomings and by keeping in mind the FAIR (findability, accessibility, interoperability, reusability) data principles, we have developed a workflow for building and analyzing biochemical pathway models, using pre-existing tools that could be utilized for the storage and refinement of models in all phases of development. We have chosen the SBtab format which allows the storage of biochemical models and associated data in a single file and provides a human readable set of syntax rules. Next, we implemented custom-made MATLAB® scripts to perform parameter estimation and global sensitivity analysis used in model refinement. Additionally, we have developed a web-based application for biochemical models that allows simulations with either a network free solver or stochastic solvers and incorporating geometry. Finally, we illustrate convertibility and use of a biochemical model in a biophysically detailed single neuron model by running multiscale simulations in NEURON. Using this workflow, we can simulate the same model in three different simulators, with a smooth conversion between the different model formats, enhancing the characterization of different aspects of the model.

Mathematical assessment of constant and time-dependent control measures on the dynamics of the novel coronavirus: An application of optimal control theory

The coronavirus infectious disease (COVID-19) is a novel respiratory disease reported in 2019 in China. The COVID-19 is one of the deadliest pandemics in history due to its high mortality rate in a short period. Many approaches have been adopted for disease minimization and eradication. In this paper, we studied the impact of various constant and time-dependent variable control measures coupled with vaccination on the dynamics of COVID-19. The optimal control theory is used to optimize the model and set an effective control intervention for the infection. Initially, we formulate the mathematical epidemic model for the COVID-19 without variable controls. The model basic mathematical assessment is presented. The nonlinear least-square procedure is utilized to parameterize the model from actual cases reported in Pakistan. A well-known technique based on statistical tools known as the Latin-hypercube sampling approach (LHS) coupled with the partial rank correlation coefficient (PRCC) is applied to present the model global sensitivity analysis. Based on global sensitivity analysis, the COVID-19 vaccine model is reformulated to obtain a control problem by introducing three time dependent control variables for isolation, vaccine efficacy and treatment enhancement represented byu 1 ( t ) ,u 2 ( t ) andu 3 ( t ) , respectively. The necessary optimality conditions of the control problem are derived via the optimal control theory. Finally, the simulation results are depicted with and without variable controls using the well-known Runge-Kutta numerical scheme. The simulation results revealed that time-dependent control measures play a vital role in disease eradication.

Investigating the potential of Morris algorithm for improving the computational constraints of global sensitivity analysis

Sensitivity analysis (SA) is widely acknowledged as advantageous and worthwhile in recognizing parameters for model calibration and optimization, especially in complex hydrological models. Although Sobol global SA is an efficient way to evaluate the sensitivity indices, the computational cost is a constraint. This study analyzes the potential of Morris global SA to achieve results tantamount to Sobol SA, at a much cheaper computational expense, using a new approach of increasing the number of replications for the Morris algorithm. SA for two catchments is performed on a coupled hydrological model using Morris and Sobol algorithms. Two target functions are used for each of the algorithms. Sobol SA required 660000 model simulations accounting for about 400 computing hours, whereas increasing the replications from 1000 to 3000, the Morris method called for 63000 runs and 06 computing hours to produce significantly similar results. The Morris parameter ranking improved 50% with respect to Sobol SA by a three-fold increase in replications with a small 5-h increase in the computational expense. The results also suggest that target functions and catchments influence parameter sensitivity. The new approach to employ the Morris method of SA shows promising results for highly parameterized hydrological models without compromising the quality of SA, specifically if there are time constraints. The study encourages the use of SA, which is mainly skipped because of higher computational demands.

Ranking non-pharmaceutical interventions against Covid-19 global pandemic using global sensitivity analysis-Effect on number of deaths

In this study, we use Global Sensitivity Analysis (GSA) to rank four non-pharmaceutical interventions (NPIs) in a deterministic compartmental model that might control Covid-19 related deaths in the United States. The NPIs are social distancing, isolation of infected individuals, identifying asymptomatically infected individuals through testing, and the use of face masks. The model uses a fear-based behavioral model that leads unmasked susceptible individuals to wear masks. The model parameters are estimated from the reported deaths for the United States of America from March 1, 2020 to November 26, 2020. Two GSA tools, the Sobol' sesntivity indices and Partial Rank Correlation Coefficient are used to obtain the rankings of the input parameters at different stages of the disease propagation. We found that social distancing and outward mask efficiency alone decreases the output uncertainty by 25-45%. Sobol' second order indices show that the combined effect of social distancing with increased mask usage and identifying and isolating asymptomatically infected individuals decreases uncertainty an additional 10%.

Efficacy of quantifying marker-cluster rigidity in a multi-segment foot model: a Monte-Carlo based global sensitivity analysis and regression model

Marker-based clinical gait analysis and multi-segment foot models (MSFM) have been successfully used for the diagnosis and clinical management of various lower limb disorders. The accuracy and validity of the kinematics measured depend on the design of the model, as well as on the adherence to its inherent rigid body assumption. This study applies a Monte-Carlo based global sensitivity analysis to evaluate the efficacy of using 'rigid body error (σRBE)' in quantifying the rigidity of a MSFM marker-cluster. A regression model is proposed. It is concluded that σRBE is effective in quantifying rigidity.

Investigation of the importance of different factors of flood inundation modeling applied in urbanized area with variance-based global sensitivity analysis

Flood modeling provides useful information to support flood risk assessment and management and reduce flood impacts in urbanized area. The accuracy of urban flood simulation results is highly dependent on the quality of input data for which the appropriate values are generally difficult to determine for complex urbanized environment and from which various uncertainties are induced into the modeling procedure. In this study, variance-based global sensitivity analysis is applied for the hydrodynamic modeling of urban flood to explore the relative importance of the factors of interest as model inputs and their contributions to the final results of the numerical model for different outputs. The factors include the spatial resolution, the forcing condition and the characteristics of the underlying urbanized surface. The global sensitivity analysis results are examined in both spatially lumped and distributed perspective. Findings indicate that importance of the input factors varies with regard to different model output and the influence of the spatial resolution is more tightly related to the flood flow movements whereas that of the rainfall inputs is more relevant to the flood water volume. Spatial variability in the influence of the input factors is revealed to be hidden by the spatially lumped results and the importance of the factors describing the underlying urban surface is found to be largely dependent on the location of the analyzed model output associated with the land-use type. Improved understanding of sensitivity of hydrodynamic modeling of urban floods may help the modelers to decide which input factors to prioritize on according to which model outputs are assessed and where they are assessed.

A latent variable approach to account for correlated inputs in global sensitivity analysis

In drug development decision-making is often supported through model-based methods, such as physiologically-based pharmacokinetics (PBPK). Global sensitivity analysis (GSA) is gaining use for quality assessment of model-informed inference. However, the inclusion and interpretation of correlated factors in GSA has proven an issue. Here we developed and evaluated a latent variable approach for dealing with correlated factors in GSA. An approach was developed that describes the correlation between two model inputs through the causal relationship of three independent factors: the latent variable and the unique variances of the two correlated parameters. The latent variable approach was applied to a set of algebraic models and a case from PBPK. Then, this method was compared to Sobol’s GSA assuming no correlations, Sobol’s GSA with groups and the Kucherenko approach. For the latent variable approach, GSA was performed with Sobol’s method. By using the latent variable approach, it is possible to devise a unique and easy interpretation of the sensitivity indices while maintaining the correlation between the factors. Compared methods either consider the parameters independent, group the dependent variables into one unique factor or present difficulties in the interpretation of the sensitivity indices. In situations where GSA is called upon to support model-informed decision-making, the latent variable approach offers a practical method, in terms of ease of implementation and interpretability, for applying GSA to models with correlated inputs that does not violate the independence assumption. Prerequisites and limitations of the approach are discussed.

Landfill mining in Europe: Assessing the economic potential of value creation from generated combustibles and fines residue

Previous studies showed that resources recovery through landfill mining (LFM) is generally challenging from an economic perspective and that a large share of project costs is related to the external treatment and disposal of bulk process wastes such as combustibles and fines residue. Building on these analyses, this study aims to explore the potential for improving the economy of LFM in Europe by creating value from these bulk process wastes. Specifically, the combustibles are treated through internal incineration with subsequent energy recovery, while fines residue is utilized as construction aggregates. These explored possibilities are investigated considering other varying factors at the site, project, and system levels that cover possible LFM project settings in Europe. A set-based modelling approach is adapted to generate multiple LFM scenarios (531,441) and investigate the underlying critical factors that drive the economy of LFM through global sensitivity analysis. Results show that an additional 16% of LFM scenarios become net profitable, mainly driven by fines residue utilization. Avoided costs for re-landfilling are higher than the revenues from construction aggregates. By contrast, internal incineration is driven by the revenues from recovered energy rather than the avoided gate fee, which is substituted by the costs for building and operating own plants. Overall, the policy conditions remain critical to further improve the economy of LFM in Europe. Recommendations include an inclusive quality standard that relies on pollutant leachability rather than total concentration for higher-value application of fines residue and incentive rather than taxation for producing renewable energy from the combustibles.

Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models

Background

Genome-wide reconstructions of metabolism opened the way to thorough investigations of cell metabolism for health care and industrial purposes. However, the predictions offered by Flux Balance Analysis (FBA) can be strongly affected by the choice of flux boundaries, with particular regard to the flux of reactions that sink nutrients into the system. To mitigate possible errors introduced by a poor selection of such boundaries, a rational approach suggests to focus the modeling efforts on the pivotal ones.

Methods

In this work, we present a methodology for the automatic identification of the key fluxes in genome-wide constraint-based models, by means of variance-based sensitivity analysis. The goal is to identify the parameters for which a small perturbation entails a large variation of the model outcomes, also referred to as sensitive parameters. Due to the high number of FBA simulations that are necessary to assess sensitivity coefficients on genome-wide models, our method exploits a master-slave methodology that distributes the computation on massively multi-core architectures. We performed the following steps: (1) we determined the putative parameterizations of the genome-wide metabolic constraint-based model, using Saltelli’s method; (2) we applied FBA to each parameterized model, distributing the massive amount of calculations over multiple nodes by means of MPI; (3) we then recollected and exploited the results of all FBA runs to assess a global sensitivity analysis.

Results

We show a proof-of-concept of our approach on latest genome-wide reconstructions of human metabolism Recon2.2 and Recon3D. We report that most sensitive parameters are mainly associated with the intake of essential amino acids in Recon2.2, whereas in Recon 3D they are associated largely with phospholipids. We also illustrate that in most cases there is a significant contribution of higher order effects.

Conclusion

Our results indicate that interaction effects between different model parameters exist, which should be taken into account especially at the stage of calibration of genome-wide models, supporting the importance of a global strategy of sensitivity analysis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04002-0.

Dynamical analysis of the fission yeast cell cycle via Markov chain

The cell cycle is a complex network involved in the regulation of cell growth and proliferation. Intrinsic molecular noise in gene expression in the cell cycle network can generate fluctuations in protein concentration. How the cell cycle network maintains its robust transitions between cell cycle phases in the presence of these fluctuations remains unclear. To understand the complex and robust behavior of the cell cycle system in the presence of intrinsic noise, we developed a Markov model for the fission yeast cell cycle system. We quantified the effect of noise on gene and protein activity and on the probability of transition between different phases of the cell cycle. Our analysis shows how network perturbations decide the fate of the cell. Our model predicts that the cell cycle pathway (subsequent transitions from [Formula: see text]) is the most robust and probable pathway among all possible trajectories in the cell cycle network. We performed a sensitivity analysis to find correlations between protein interaction weights and transition probabilities between cell cycle phases. The sensitivity analysis predicts how network perturbations affect the transition probability between different cell cycle phases and, consequently, affect different cell fates, thus, forming testable in vitro/in vivo hypotheses. Our simulation results agree with published experimental findings and reveal how noise in the cell cycle regulatory network can affect cell cycle progression.

A conjunctive management framework for the optimal design of pumping and injection strategies to mitigate seawater intrusion

Coastal aquifer management (CAM) considering conjunctive optimization of pumping and injection system for seawater intrusion (SI) mitigation poses significant decision-making challenges. CAM needs to pose multiple objectives and massive decision variables to explore tradeoff strategies between the conflicting resources, economic, and environmental requirements. Here, we investigate a joint artificial injection scheme for ameliorating SI by establishing an evolutionary multi-objective decision-making framework that combines simulation-optimization (S-O) modelling with a cost-benefit analysis, and demonstrate the framework on a large-scale CAM case in Baldwin County, Alabama. First, a SI numerical model, using SEAWAT, was configured to predict the vulnerable region as an SI encroachment area with the scenarios of minimum and maximum pumping capacity. As a result, a smaller number of candidate sites were selected in the SI encroachment area for implementing groundwater injection to avoid the computationally infeasible SI optimization with an inordinate number of injection related decision variables. Second, the effective S-O methodology of niched Pareto tabu search combined with a genetic algorithm (NPTSGA), which considers the moving-well option, was applied to discover optimal pumping/injection (P/I) strategies (including P/I rates and injection well locations) between three conflicting management objectives under complicated SI constraints. Third, for practical operation of the P/I schemes, a cost-benefit analysis provides judgment criteria to allow decision-makers to implement more sustainable P/I strategies to capture the different realistic preferences. The implementation of three extreme optimization solutions for the case study indicates that, compared to the initial unoptimized scheme, a maximum increase of a factor of 3 in groundwater extraction rates, a maximum reduction of 17% in extent of SI, and a maximum 82.3 million US dollars in comprehensive benefits are specifically achieved by conjunctive P/I optimization. The robustness in the decision alternatives attributed to the uncertainty in physical parameters of hydraulic conductivity was discovered through global sensitivity analysis. The proposed framework provides a decision support system for multi-objective CAM with combined pumping control and engineering measures for SI mitigation.

Surrogate based Global Sensitivity Analysis of ADM1-based Anaerobic Digestion Model

In order to calibrate the model parameters, Sensitivity Analysis routines are mandatory to rank the parameters by their relevance and fix to nominal values the least influential factors. Despite the high number of works based on ADM1, very few are related to sensitivity analysis. In this study Global Sensitivity Analysis (GSA) and Uncertainty Quantification (UQ) for an ADM1-based Anaerobic Digestion Model have been performed. The modified version of ADM-based model selected in this study was presented by Esposito and co-authors in 2013. Unlike the first version of ADM1, focused on sewage sludge degradation, the model of Esposito is focused on organic fraction of municipal solid waste digestion. It his recalled that in many applications the hydrolysis is considered the bottleneck of the overall anaerobic digestion process when the input substrate is constituted of complex organic matter. In Esposito's model a surfaced based kinetic approach for the disintegration of complex organic matter is introduced. This approach allows to better model the disintegration step taking into account the effect of particle size distribution on the digestion process. This model needs thus GSA and UQ to pave the way for further improvements and reach a deep understanding of the main processes and leading input factors. Due to the large number of parameters to be analyzed a first preliminary screening analysis, with the Morris' Method, has been conducted. Since two quantities of interest (QoI) have been considered, the initial screening has been performed twice, obtaining two set of parameters containing the most influential factors in determining the value of each QoI. A surrogate of ADM1 model has been defined making use of the two defined quantities of interest. The output results from the surrogate model have been analyzed with Sobol' indices for the quantitative GSA. Finally, uncertainty quantification has been performed. By adopting kernel smoothing techniques, the Probability Density Functions of each quantity of interest have been defined.

Coasting: Model description, global sensitivity analysis, and scenario discovery

This manuscript provides information for replicating the Coasting agent-based model presented in “Simulating emerging coastal tourism vulnerabilities: an agent-based modelling approach”. The model description follows the Overview, Design Concepts, and Details + Human Decision-making (ODD+D) protocol. Moreover, this paper includes implementation details on global sensitivity analysis and scenario discovery. Finally, we provide supplementary tables and figures for scenario discovery results not included in the main paper.



Highlights:

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Model description for simulating emerging environmental vulnerabilities in a coastal tourism context

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Coasting’s design facilitates model adaptations to other coastal tourism destinations

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Implementation details for applying global sensitivity analysis and scenario discovery to vulnerability assessments

A mechanistic effect modeling approach to the prioritization of hidden drivers in chemical cocktails

Exposure to a single chemical does not exist in reality. Mixtures, which are the ecological norm, are often characterized by numerous intrinsic driving factors with unknown combined effects. Interactions between heterogeneous chemicals, or chemical and nonchemical stressors, could alter their toxicity traits relative to single exposure. Hence, revealing the hidden environmental effects affecting multiple stressor interactions is essential to expand our knowledge about uncertainty sources in chemical risk-based decision contexts. Global sensitivity analysis (GSA) techniques involving Morris method sampling and elementary effects (EE) sensitivity analysis was applied to investigate the driving factors underlying the combined effects on Scenedesmus obliquus, and identify the mode of interaction in mixtures at environmentally-relevant concentrations. One hundred mixed-exposure formulas were generated with 9 variables (8 chemicals and temperature) via the Morris method, representing environmental perspective in the field. Subsequently, EE sensitivity analysis combined with quantitative high-throughput screening (q-HTS) was adopted to identify the most critical mixture and its primary drivers. Combined exposure exerted significantly increased effects on S. obliquus compared to the effects of individual exposure. The critical drivers were identified and validated by the control variate method. For the mode of combined action, mixture toxicity did not match the additivity relationship, and a strong interaction existed among chemicals. Collectively, the data provides evidence that a combination of specific pesticides and emerging brominated flame retardants can produce comparable, or even stronger, bionegative effects than pure chemicals due to complicated interactions. The method used offers direct comparison of multifarious factors in a unified standard scale, bridges the actual interaction scenarios in the field to toxicity simulations in the laboratory, and fill a gap in ecotoxicology.

Modeling the impact of non-pharmaceutical interventions on the dynamics of novel coronavirus with optimal control analysis with a case study

Coronavirus disease (COVID-19) is the biggest public health challenge the world is facing in recent days. Since there is no effective vaccine and treatment for this virus, therefore, the only way to mitigate this infection is the implementation of non-pharmaceutical interventions such as social-distancing, community lockdown, quarantine, hospitalization or self-isolation and contact-tracing. In this paper, we develop a mathematical model to explore the transmission dynamics and possible control of the COVID-19 pandemic in Pakistan, one of the Asian countries with a high burden of disease with more than 200,000 confirmed infected cases so far. Initially, a mathematical model without optimal control is formulated and some of the basic necessary analysis of the model, including stability results of the disease-free equilibrium is presented. It is found that the model is stable around the disease-free equilibrium both locally and globally when the basic reproduction number is less than unity. Despite the basic analysis of the model, we further consider the confirmed infected COVID-19 cases documented in Pakistan from March 1, till May 28, 2020 and estimate the model parameters using the least square fitting tools from statistics and probability theory. The results show that the model output is in good agreement with the reported COVID-19 infected cases. The approximate value of the basic reproductive number based on the estimated parameters is R 0 ≈ 1.87 . The effect of low (or mild), moderate, and comparatively strict control interventions like social-distancing, quarantine rate, (or contact-tracing of suspected people) and hospitalization (or self-isolation) of testing positive COVID-19 cases are shown graphically. It is observed that the most effective strategy to minimize the disease burden is the implementation of maintaining a strict social-distancing and contact-tracing to quarantine the exposed people. Furthermore, we carried out the global sensitivity analysis of the most crucial parameter known as the basic reproduction number using the Latin Hypercube Sampling (LHS) and the partial rank correlation coefficient (PRCC) techniques. The proposed model is then reformulated by adding the time-dependent control variables u ₁(t) for quarantine and u ₂(t) for the hospitalization interventions and present the necessary optimality conditions using the optimal control theory and Pontryagin's maximum principle. Finally, the impact of constant and optimal control interventions on infected individuals is compared graphically.

Considerations and Caveats when Applying Global Sensitivity Analysis Methods to Physiologically Based Pharmacokinetic Models

Three global sensitivity analysis (GSA) methods (Morris, Sobol and extended Sobol) are applied to a minimal physiologically based PK (mPBPK) model using three model drugs given orally, namely quinidine, alprazolam, and midazolam. We investigated how correlations among input parameters affect the determination of the key parameters influencing pharmacokinetic (PK) properties of general interest, i.e., the maximal plasma concentration (C_max) time at which C_max is reached (T_max), and area under plasma concentration (AUC). The influential parameters determined by the Morris and Sobol methods (suitable for independent model parameters) were compared to those determined by the extended Sobol method (which considers model parameter correlations). For the three drugs investigated, the Morris method was as informative as the Sobol method. The extended Sobol method identified different sets of influential parameters to Morris and Sobol. These methods overestimated the influence of volume of distribution at steady state (V_ss) on AUC24h for quinidine and alprazolam. They also underestimated the effect of volume of liver (V_liver) for all three drugs, the impact of enzyme intrinsic clearance of CYP2C9 and CYP2E1 for quinidine, and that of UGT1A4 abundance for midazolam. Our investigation showed that the interpretation of GSA results is not straightforward. Dismissing existing model parameter correlations, GSA methods such as Morris and Sobol can lead to biased determination of the key parameters for the selected outputs of interest. Decisions regarding parameters’ influence (or otherwise) should be made in light of available knowledge including the model assumptions, GSA method limitations, and inter-correlations between model parameters, particularly in complex models.

pksensi: An R package to apply global sensitivity analysis in physiologically based kinetic modeling

Sensitivity analysis (SA) is an essential tool for modelers to understand the influence of model parameters on model outputs. It is also increasingly used in developing and assessing physiologically based kinetic (PBK) models. For instance, several studies have applied global SA to reduce the computational burden in the Bayesian Markov chain Monte Carlo-based calibration process PBK models. Although several SA algorithms and software packages are available, no comprehensive software package exists that allows users to seamlessly solve differential equations in a PBK model, conduct and visualize SA results, and discriminate between the non-influential model parameters that can be fixed and those that need calibration. Therefore, we developed an R package, named pksensi, to make global SA more accessible in PBK modeling. This package can investigate both uncertainty and sensitivity in PBK models, including those with multivariate model outputs. It also includes functions to check the convergence of the global SA results. Overall, pksensi improves the user experience of performing global SA and can create robust and reproducible results for decision making in PBK model calibration.

Sobol sensitivity analysis for risk assessment of uranium in groundwater

The exposure to uranium (U) in the natural environment is primarily through ingestion (eating contaminated food and drinking water) and dermal (skin contact with U powders/wastes) pathways. This study focuses on the dose assessment for different age-groups using the USEPA model. A total of 156 drinking water samples were tested to know U level in the groundwater of the study region. Different age-groups were selected to determine the human health impact due to uranium exposure in the residing populations. To determine the relative importance of each input, a variance decomposition technique, i.e., Sobol sensitivity analysis, was used. Furthermore, different sample sizes were tested to obtain the optimal Sobol sensitivity indices. Three types of effects were evaluated: first-order effect (FOE), second-order effect (SOE) and total effect. The result of analysis revealed that 17% of the samples had U concentration above 30 µg l^-1 of U, which is the recommended level by World Health Organization. The mean hazard index (HI) value for younger age-group was found to be less than 1, whereas the 95th percentile value of HI value exceeded for both age-groups. The mean annual effective dose of U for adults was found to be slightly higher than the recommended level of 0.1 m Sv year^-1. This result signified that adults experienced relatively higher exposure dose than the children in this region. Sobol sensitivity analysis of FOE showed that the concentration of uranium (C_w) is the most sensitive input followed by intake rate (IR) and exposure frequency. Moreover, the value of SOE revealed that interaction effect of C_w- IR is the most sensitive input parameter for the assessment of oral health risk. On the other hand, dermal model showed C_w- F as the most sensitive interaction input. The larger value of SOE was also recorded for older age-group than for the younger group.

A cyberGIS approach to spatiotemporally explicit uncertainty and global sensitivity analysis for agent-based modeling of vector-borne disease transmission

While agent-based models (ABMs) provide an effective means for investigating complex interactions between heterogeneous agents and their environment, they may hinder an improved understanding of phenomena being modeled due to inherent challenges associated with uncertainty in model parameters. This study uses uncertainty analysis and global sensitivity analysis (UA-GSA) to examine the effects of such uncertainty on model outputs. The statistics used in UA-GSA, however, are likely to be affected by the modifiable areal unit problem (MAUP). Therefore, to examine the scale varying-effects of model inputs, UA-GSA needs to be performed at multiple spatiotemporal scales. Unfortunately, performing comprehensive UA-GSA comes with considerable computational cost. In this paper, our cyberGIS-enabled spatiotemporally explicit UA-GSA approach helps to not only resolve the computational burden, but also to measure dynamic associations between model inputs and outputs. A set of computational and modeling experiments shows that input factors have scale-dependent impacts on modeling output variability. In other words, most of the input factors have relatively large impacts in a certain region, but may not influence outcomes in other regions. Furthermore, our spatiotemporally explicit UA-GSA approach sheds light on the effects of input factors on modeling outcomes that are particularly spatially and temporally clustered, such as the occurrence of communicable disease transmission.

An open source physiologically based kinetic model for the chicken (Gallus gallus domesticus): Calibration and validation for the prediction residues in tissues and eggs

Xenobiotics from anthropogenic and natural origin enter animal feed and human food as regulated compounds, environmental contaminants or as part of components of the diet. After dietary exposure, a chemical is absorbed and distributed systematically to a range of organs and tissues, metabolised, and excreted. Physiologically based kinetic (PBK) models have been developed to estimate internal concentrations from external doses. In this study, a generic multi-compartment PBK model was developed for chicken. The PBK model was implemented for seven compounds (with log K_ow range -1.37-6.2) to quantitatively link external dose and internal dose for risk assessment of chemicals. Global sensitivity analysis was performed for a hydrophilic and a lipophilic compound to identify the most sensitive parameters in the PBK model. Model predictions were compared to measured data according to dataset-specific exposure scenarios. Globally, 71% of the model predictions were within a 3-fold change of the measured data for chicken and only 7% of the PBK predictions were outside a 10-fold change. While most model input parameters still rely on in vivo experiments, in vitro data were also used as model input to predict internal concentration of the coccidiostat monensin. Future developments of generic PBK models in chicken and other species of relevance to animal health risk assessment are discussed.

Development and evaluation of a process-based model to assess nutrient removal in floating treatment wetlands

Modelling is a useful tool for comprehensively describing the processes occurring in floating treatment wetlands (FTWs). However, temperature effects and phosphorus dynamics are not considered in the current FTW models. Therefore, a process-based model comprised of a plant growth submodel, a nitrogen dynamic submodel and a phosphorus dynamic submodel was developed to understand the complicated processes occurring in FTWs. The model was fully calibrated using a mesocosm FTW system operated for 168 days. Global sensitivity analysis revealed that nitrogen removal performance was predominantly sensitive to parameters representing plant characteristics and microbial activity. Because of the high concentration of organic matter, mineralization and sedimentation played important roles in nitrogen and phosphorus removal. In addition, the coprecipitation rate of phosphate also had a significant influence on phosphorus removal performance. When further investigation was applied to understand the behavior of the model, the ratio of nitrogen to phosphorus in plant tissue was found to be an indicator of the nutrient limitation in the water column. Furthermore, the model illustrated that both FTW operating conditions and plant characteristic parameters exerted an important influence on nitrogen removal and plant uptake contribution. Therefore, the selection of appropriate operating conditions and plant species can achieve high nutrients removal and make effective use of plants in FTWs. The model provides a useful tool for assessing the nutrients removal performance of FTWs and for evaluating strategies for them in design and operation.

Assessing practical identifiability during calibration and cross-validation of a structured model for high-solids anaerobic digestion

High-solids anaerobic digestion (HS-AD) of the organic fraction of municipal solid waste (OFMSW) is operated at a total solid (TS) content ≥ 10% to enhance the waste treatment economy, though it might be associated to free ammonia (NH₃) inhibition. This study aimed to calibrate and cross-validate a HS-AD model for homogenized reactors in order to assess the effects of high NH₃ levels in HS-AD of OFMSW, but also to evaluate the suitability of the reversible non-competitive inhibition function to reproduce the effect of NH₃ on the main acetogenic and methanogenic populations. The practical identifiability of structural/biochemical parameters (i.e. 35) and initial conditions (i.e. 32) was evaluated using batch experiments at different TS and/or inoculum-to-substrate ratios. Variance-based global sensitivity analysis and approximate Bayesian computation were used for parameter optimization. The experimental data in this study permitted to estimate up to 8 biochemical parameters, whereas the rest of parameters and biomass contents were poorly identifiable. The study also showed the relatively high levels of NH₃ (i.e. up to 2.3 g N/L) and ionic strength (i.e. up to 0.9 M) when increasing TS in HS-AD of OFMSW. However, the NH₃ non-competitive function was unable to capture the acetogenic/methanogenic inhibition. Therefore, the calibration emphasized the need for target-oriented experimental data to enhance the practical identifiability and the predictive capabilities of structured HS-AD models, but also the need for further testing the NH₃ inhibition function used in these simulations.

Systematic assessment of critical factors for the economic performance of landfill mining in Europe: What drives the economy of landfill mining?

Landfill mining (LFM) is a strategy to mitigate environmental impacts associated with landfills, while simultaneously recovering dormant materials, energy carriers, and land resources. Although several case study assessments on the economy of LFM exist, a broader understanding of the driving factors is still lacking. This study aims at identifying generically important factors for the economy of LFM in Europe and understanding their role in developing economically feasible projects in view of different site, project and system-level conditions. Therefore, a set-based modeling approach is used to establish a large number (531,441) of LFM scenarios, evaluate their economic performance in terms of net present value (NPV), and analyze the relationships between input factors and economic outcome via global sensitivity analysis. The scenario results range from -139 Euro to +127 Euro/Mg of excavated waste, with 80% of the scenarios having negative NPVs. Variations in the costs for waste treatment and disposal and the avoided cost of alternative landfill management (i.e. if the landfill was not mined) have the strongest effect on the scenario NPVs, which illustrates the critical role of system level factors for LFM economy and the potential of policy intervention to incentivize LFM. Consequently, system conditions should guide site selection and project development, which is exemplified in the study for two extreme regional archetypes in terms of income and waste management standard. Future work should further explore the developed model to provide decision support on LFM strategies in consideration of alternative purposes, stakeholders, and objectives.