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opencc-zeroDec 2019View details →

Supplementary material 2 from: Desvignes V, Buschhardt T, Guillier L, Sanaa M (2019) Quantitative microbial risk assessment for Salmonella in eggs. Food Modelling Journal 1: e39643. https://doi.org/10.3897/fmj.1.39643

Parameter settings

opencc-zeroDec 2019View details →

Supplementary material 1 from: Desvignes V, Buschhardt T, Guillier L, Sanaa M (2019) Quantitative microbial risk assessment for Salmonella in eggs. Food Modelling Journal 1: e39643. https://doi.org/10.3897/fmj.1.39643

QMRA_Salmonella_egg_Virginie.fskx

opencc-by-4.0Jan 2020View details →

Figure 2 from: Desvignes V, Buschhardt T, Guillier L, Sanaa M (2019) Quantitative microbial risk assessment for Salmonella in eggs. Food Modelling Journal 1: e39643. https://doi.org/10.3897/fmj.1.39643

Figure 2 Predicted number of salmonellosis per million servings of eggs, according to the cooking method.

opencc-by-4.0Jun 2020View details →

Brumadinho tailings dam, Brazil model animations of mudflow and risk to people plus GIS files

The data set comprises animations of modelling the mudflow and risks to people carried out of the Brumadinho tailings dam failure which occurred in January 2019. Some additional GIS files are also included.

opencc-by-4.0Jun 2020View details →

Development and validation of a machine learning model for use as an automated artificial intelligence tool to predict mortality risk in patients with COVID-19

Background New York City quickly became an epicenter of the COVID-19 pandemic. Due to a sudden and massive increase in patients during COVID-19 pandemic, healthcare providers incurred an exponential increase in workload which created a strain on the staff and limited resources. As this is a new infection, predictors of morbidity and mortality are not well characterized. Methods We developed a prediction model to predict patients at risk for mortality using only laboratory, vital and demographic information readily available in the electronic health record on more than 3000 hospital admissions with COVID-19. A variable importance algorithm was used for interpretability and understanding of performance and predictors. Findings We built a model with 84-97% accuracy to identify predictors and patients with high risk of mortality, and developed an automated artificial intelligence (AI) notification tool that does not require manual calculation by the busy clinician. Oximetry, respirations, blood urea nitrogen, lymphocyte percent, calcium, troponin and neutrophil percentage were important features and key ranges were identified that contributed to a 50% increase in patients’ mortality prediction score. With an increasing negative predictive value (NPV) starting 0.90 after the second day of admission, we are able more confidently able identify likely survivors. This study serves as a use case of a model with visualizations to aide clinicians with a better understanding of the model and predictors of mortality. Additionally, an example of the operationalization of the model via an AI notification tool is illustrated.

opencc-zeroSep 2020View details →

Raw in vitro screening data and R scripts for: A Bayesian method for population-wide cardiotoxicity hazard and risk characterization using an in vitro human model

Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes are an established model for testing potential chemical hazards. Inter-individual variability in toxicodynamic sensitivity has also been demonstrated in vitro; however, quantitative characterization of the population-wide variability has not been fully explored. We sought to develop a method to address this gap by combining a population-based iPSC-derived cardiomyocyte model with Bayesian concentration-response modeling. A total of 136 compounds, including 44 pharmaceuticals and 82 environmental chemicals, were tested in iPSC-derived cardiomyocytes from 43 non-diseased humans. Hierarchical Bayesian population concentration-response modeling was conducted for five phenotypes reflecting cardiomyocyte function or viability. Toxicodynamic variability was quantified through the derivation of chemical- and phenotype-specific variability factors (TDVF). Toxicokinetic modeling was used for probabilistic in vitro-to-in vivo extrapolation in order to derive population-wide margins of safety (MOS) for pharmaceuticals and margins of exposure (MOE) for environmental chemicals. Pharmaceuticals were found to be active across all phenotypes. Over half of tested environmental chemicals showed activity in at least one phenotype, most commonly positive chronotropy. TDVF estimates for the functional phenotypes were greater than those for cell viability, usually exceeding the generally-assumed default of ~3. Population variability-based MOS for pharmaceuticals were correctly predicted to be relatively narrow, between 10-100; however, MOE for environmental chemicals, based on population exposure estimates, generally exceeded 1000, suggesting they pose little risk at general population exposures even to sensitive sub populations. This study represents a first of its kind human in vitro model that can be used to characterize toxicodynamic population variability in cardiotoxic risk.

opencc-zeroNov 2020View details →

Data from: A predictive model for improving placement of wind turbines to minimise collision risk potential for a large soaring raptor

1. With the rapid growth of wind energy developments worldwide, it is critical that the negative impacts on wildlife are considered and mitigated. This includes minimising the numbers of large soaring raptors which are killed when they collide with wind turbines. 2. To reduce the likelihood of raptor collisions, turbines should be placed at locations which are least used by sensitive species. For resident or breeding species, this is often delineated crudely through the use of circular buffers centred on nest sites, which assume uniform habitat use around a nest site. 3. Using GPS tracking data together with a digital elevation model we build and cross-validate a simple generalizable model, to classify the spatial likelihood of wind turbine collisions for resident adult Verreaux's eagles in any landscape where there are known nests. We apply our methods to operational developments in South Africa to validate the model and demonstrate its ability in predicting actual collision mortalities. 4. Our Collision Risk Potential (CRP) model included the variables distance to nest, distance to conspecific nest, slope, distance to slope and elevation. Using our model, rather than a circular buffer, resulted in ca. 4–5% improvement in eagle protection while excluding development from the same amount (but not shape) of area. For an equal level of eagle protection, our model can make ca. 20–21% more area available for wind energy development compared to a circular buffer. 5. Exploring collisions at operational wind farms in South Africa we show that our CRP model correctly predicted 87% of known collisions, while circular buffers (5.2km radius) only captured 50% of collisions. 6. Synthesis and applications: We show that by using predictive models to account for habitat use, a greater area of land can be made available for wind energy development without increased mortality risk to raptors. Our predictive model can be used to provide robust guidance on wind turbine placement in South Africa in a way which minimizes the conflict between a vulnerable raptor species and the development of renewable energy.

opencc-zeroDec 2020View details →

Drought risk of global terrestrial gross primary productivity in recent 40 years detected by a remote sensing-driven process model

Gross primary productivity (GPP) is the largest flux in the global terrestrial carbon cycle and affected by multiple factors. In recent decades, drought has significantly impacted global terrestrial GPP and been projected to occur with increasing frequency and intensity. However, the drought risk of global terrestrial GPP has not been well investigated. In this study, global terrestrial GPP over the period from 1981 to 2016 was simulated with the process-based Boreal Ecosystem Productivity Simulator (BEPS) model. Then, the drought risk of terrestrial GPP was quantified as the product of frequency of drought and reduction of GPP caused by drought, which were determined using the standardized precipitation evapotranspiration index (SPEI). During the study period, the drought risk of terrestrial GPP exhibited detectable spatial heterogeneity, high in southeastern United States, most of South America, southern Europe, central and eastern Africa, eastern and southeastern Asia, and eastern Australia. In these regions, the maximum reduction of GPP might be above 30% in drought years relative to that in normal years. The drought risk of GPP was low at high latitudes of the Northern Hemisphere, in which terrestrial GPP increased slightly in drought years. The spatial pattern of the drought risk of GPP simulated by the BEPS model was close to that of FLUXCOM GPP, which was scaled from tower observations with a machine learning algorithm forced by remote sensing and meteorological data. This study advances our understanding on the impact of drought on terrestrial GPP over the globe.

opencc-by-4.0Oct 2023View details →

COVINFORM Risk Model Framework

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openDec 2023View details →

Wildfire Risk Assessment for Strategic Forest Management in the Southern United States: a Bayesian Network Modeling Approach

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opencc-zeroMar 2024View details →

Supplementary material 1 from: Basak S, Christy J, Guillier L, Audiat-Perrin F, Sanaa M, Tenenhaus-Aziza F, Bect J, Vazquez E (2024) Quantitative risk assessment of Haemolytic and Uremic Syndrome (HUS) from consumption of raw milk soft cheese. Food and Ecological Systems Modelling Journal 5: e109502. https://doi.org/10.3897/fmj.5.109502

QRA simulator

Figure 6 from: Basak S, Christy J, Guillier L, Audiat-Perrin F, Sanaa M, Tenenhaus-Aziza F, Bect J, Vazquez E (2024) Quantitative risk assessment of Haemolytic and Uremic Syndrome (HUS) from consumption of raw milk soft cheese. Food and Ecological Systems Modelling Journal 5: e109502. https://doi.org/10.3897/fmj.5.109502

Figure 6 The relative batch risk (with respect to a baseline risk value) is plotted as a function of the initial STEC (main pathogenic serotypes MPS-STEC) concentration (CFU/ml).

Figure 5 from: Basak S, Christy J, Guillier L, Audiat-Perrin F, Sanaa M, Tenenhaus-Aziza F, Bect J, Vazquez E (2024) Quantitative risk assessment of Haemolytic and Uremic Syndrome (HUS) from consumption of raw milk soft cheese. Food and Ecological Systems Modelling Journal 5: e109502. https://doi.org/10.3897/fmj.5.109502

Figure 5 Batch rejection probability as a function of the initial STEC (main pathogenic serotypes MPS-STEC) concentration (CFU/ml).

Figure 4 from: Basak S, Christy J, Guillier L, Audiat-Perrin F, Sanaa M, Tenenhaus-Aziza F, Bect J, Vazquez E (2024) Quantitative risk assessment of Haemolytic and Uremic Syndrome (HUS) from consumption of raw milk soft cheese. Food and Ecological Systems Modelling Journal 5: e109502. https://doi.org/10.3897/fmj.5.109502

Figure 4 Evolution of STEC colony size during draining, salting and ripening of cheese fabrication. The decline rate for the MPS O157:H7 strain and non-MPS strains are equal (orange line) and significantly higher than the decline rate of MPS non-O157:H7 strain (red line). The three phases, namely, draining, salting and ripening are separated by vertical blue dotted lines.

Figure 3 from: Basak S, Christy J, Guillier L, Audiat-Perrin F, Sanaa M, Tenenhaus-Aziza F, Bect J, Vazquez E (2024) Quantitative risk assessment of Haemolytic and Uremic Syndrome (HUS) from consumption of raw milk soft cheese. Food and Ecological Systems Modelling Journal 5: e109502. https://doi.org/10.3897/fmj.5.109502

Figure 3 Evolution of STEC (main pathogenic serotypes MPS-STEC) in log10 CFU/ml during the storage and moulding step. The blue vertical line shows the end of the storage phase.

Figure 2 from: Basak S, Christy J, Guillier L, Audiat-Perrin F, Sanaa M, Tenenhaus-Aziza F, Bect J, Vazquez E (2024) Quantitative risk assessment of Haemolytic and Uremic Syndrome (HUS) from consumption of raw milk soft cheese. Food and Ecological Systems Modelling Journal 5: e109502. https://doi.org/10.3897/fmj.5.109502

Figure 2 Histogram of STEC (main pathogenic serotypes MPS-STEC) concentration (log10 (CFU/ml)) in milk put into production.

Figure 1 from: Basak S, Christy J, Guillier L, Audiat-Perrin F, Sanaa M, Tenenhaus-Aziza F, Bect J, Vazquez E (2024) Quantitative risk assessment of Haemolytic and Uremic Syndrome (HUS) from consumption of raw milk soft cheese. Food and Ecological Systems Modelling Journal 5: e109502. https://doi.org/10.3897/fmj.5.109502

Figure 1 Schematic diagram of the batch level simulator of the risk assessment model. Modules are denoted by pink coloured boxes with the blue boxes denoting the set of corresponding input parameters \documentclass[12pt]{standalone} \usepackage{varwidth} \usepackage[utf8x]{inputenc} \usepackage[T1]{fontenc} \usepackage{lmodern} \usepackage{amsmath, amssymb, graphics, setspace} \newcommand{\mathsym}[1]{{}} \newcommand{\unicode}[1]{{}} \newcounter{mathematicapage} \begin{document} \begin{varwidth}{50in} \begin{equation*} \theta = \{\theta^{\rm farm}, \theta^{\rm cheese}, \theta^{\rm con}, \theta^{\rm post}\} \end{equation*} \end{varwidth} \end{document} and the orange boxes denoting the outputs, namely, milk loss per batch \documentclass[12pt]{standalone} \usepackage{varwidth} \usepackage[utf8x]{inputenc} \usepackage[T1]{fontenc} \usepackage{lmodern} \usepackage{amsmath, amssymb, graphics, setspace} \newcommand{\mathsym}[1]{{}} \newcommand{\unicode}[1]{{}} \newcounter{mathematicapage} \begin{document} \begin{varwidth}{50in} \begin{equation*} M^{\rm batch} \end{equation*} \end{varwidth} \end{document} , probability of rejecting a particular batch \documentclass[12pt]{standalone} \usepackage{varwidth} \usepackage[utf8x]{inputenc} \usepackage[T1]{fontenc} \usepackage{lmodern} \usepackage{amsmath, amssymb, graphics, setspace} \newcommand{\mathsym}[1]{{}} \newcommand{\unicode}[1]{{}} \newcounter{mathematicapage} \begin{document} \begin{varwidth}{50in} \begin{equation*} P^{\rm batch} \end{equation*} \end{varwidth} \end{document} and batch risk \documentclass[12pt]{standalone} \usepackage{varwidth} \usepackage[utf8x]{inputenc} \usepackage[T1]{fontenc} \usepackage{lmodern} \usepackage{amsmath, amssymb, graphics, setspace} \newcommand{\mathsym}[1]{{}} \newcommand{\unicode}[1]{{}} \newcounter{mathematicapage} \begin{document} \begin{varwidth}{50in} \begin{equation*} R^{\rm batch} \end{equation*} \end{varwidth} \end{document} .

opencc-zeroNov 2021View details →

External validation of EPIC's Risk of Unplanned Readmission model, the LACE+ index and SQLape® as predictors of unplanned hospital readmissions: A monocentric, retrospective, diagnostic cohort study in Switzerland

Introduction: Readmissions after an acute care hospitalization are relatively common, costly to the health care system, and are associated with significant burden for patients. As one way to reduce costs and simultaneously improve quality of care, hospital readmissions receive increasing interest from policy makers. It is only relatively recently that strategies were developed with the specific aim of reducing unplanned readmissions using prediction models to identify patients at risk. EPIC's Risk of Unplanned Readmission model promises superior performance. However, it has only been validated for the US setting. Therefore, the main objective of this study is to externally validate the EPIC's Risk of Unplanned Readmission model and to compare it to the internationally, widely used LACE+ index, and the SQLAPE® tool, a Swiss national quality of care indicator. Methods: A monocentric, retrospective, diagnostic cohort study was conducted. The study included inpatients, who were discharged between the 1st of January 2018 and the 31st of December 2019 from the Lucerne Cantonal Hospital, a tertiary-care provider in Central Switzerland. The study endpoint was an unplanned 30-day readmission. Models were replicated using the original intercept and beta coefficients as reported. Otherwise, score generator provided by the developers were used. For external validation, discrimination of the scores under investigation were assessed by calculating the area under the receiver operating characteristics curves (AUC). Calibration was assessed with the Hosmer-Lemeshow X2 goodness-of-fit test This report adheres to the TRIPOD statement for reporting of prediction models. Results: At least 23,116 records were included. For discrimination, the EPIC´s prediction model, the LACE+ index and the SQLape® had AUCs of 0.692 (95% CI 0.676-0.708), 0.703 (95% CI 0.687-0.719) and 0.705 (95% CI 0.690-0.720). The Hosmer-Lemeshow X2 tests had values of p<0.001. Conclusion: In summary, the EPIC´s model showed less favorable performance than its comparators. It may be assumed with caution that the EPIC´s model complexity has hampered its wide generalizability - model updating is warranted.