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2022 ◽  
Author(s):  
Melen Leclerc ◽  
Stéphane Jumel ◽  
Frédéric M. Hamelin ◽  
Rémi Treilhaud ◽  
Nicolas Parisey ◽  
...  

Within-host spread of pathogens is an important process for the study of plant-pathogen interactions. However, the development of plant-pathogen lesions remains practically difficult to characterize and quantify beyond the common traits such as lesion area. We tackle the spatio-temporal dynamics of interactions by combining image-based phenotyping with mathematical modelling. We consider the spread of Peyronellaea pinodes on pea stipules that were monitored daily with visible imaging. We assume that pathogen propagation on host-tissues can be described by the Fisher-KPP model where lesion spread depends on both a logistic local growth and an homogeneous diffusion. Model parameters are estimated using a variational data assimilation approach on sets of registered images. This modelling framework is used to compare the spread of an aggressive isolate on two pea cultivars with contrasted levels of partial resistance. We show that the expected slower spread on the most resistant cultivar is actually due to a decrease of diffusion and, to a lesser extent, local growth. These results demonstrate that spatial models with imaging allows one to disentangle the processes involved in host-pathogen interactions. Hence, promoting model-based phenotyping of interactions would allow a better identification of quantitative traits thereafter used in genetics and ecological studies.


2022 ◽  
Vol 13 (1) ◽  
Author(s):  
M. Springmann ◽  
F. Freund

AbstractAgricultural subsidies are an important factor for influencing food production and therefore part of a food system that is seen as neither healthy nor sustainable. Here we analyse options for reforming agricultural subsidies in line with health and climate-change objectives on one side, and economic objectives on the other. Using an integrated modelling framework including economic, environmental, and health assessments, we find that on a global scale several reform options could lead to reductions in greenhouse gas emissions and improvements in population health without reductions in economic welfare. Those include a repurposing of up to half of agricultural subsidies to support the production of foods with beneficial health and environmental characteristics, including fruits, vegetables, and other horticultural products, and combining such repurposing with a more equal distribution of subsidy payments globally. The findings suggest that reforming agricultural subsidy schemes based on health and climate-change objectives can be economically feasible and contribute to transitions towards healthy and sustainable food systems.


2022 ◽  
Author(s):  
Mohamed Abbas ◽  
Anne Cori ◽  
Samuel Cordey ◽  
Florian Laubscher ◽  
Tomás Robalo Nunes ◽  
...  

Background There is ongoing uncertainty regarding transmission chains and the respective roles of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS–CoV–2) in geriatric settings. Methods We performed a retrospective cohort study including patients with nosocomial coronavirus disease 2019 (COVID–19) in four outbreak–affected wards, and all SARS–CoV–2 RT–PCR positive HCWs from a Swiss university–affiliated geriatric acute–care hospital that admitted both Covid–19 and non–Covid–19 patients during the first pandemic wave in Spring 2020. We combined epidemiological and genetic sequencing data using a Bayesian modelling framework, and reconstructed transmission dynamics of SARS–CoV–2 involving patients and HCWs, in order to determine who infected whom. We evaluated general transmission patterns according to type of case (HCWs working in dedicated Covid–19 cohorting wards: HCWcovid; HCWs working in non–Covid–19 wards where outbreaks occurred: HCWoutbreak; patients with nosocomial Covid–19: patientnoso) by deriving the proportion of infections attributed to each type of case across all posterior trees and comparing them to random expectations. Results During the study period (March 1 to May 7, 2020) we included 180 SARS–CoV–2 positive cases: 127 HCWs (91 HCWcovid, 36 HCWoutbreak) and 53 patients. The attack rates ranged from 10–19% for patients, and 21% for HCWs. We estimated that there were 16 importation events (3 patients, 13 HCWs) that jointly led to 16 secondary cases. Most patient–to–patient transmission events involved patients having shared a ward (97.6%, 95% credible interval [CrI] 90.4–100%), in contrast to those having shared a room (44.4%, 95%CrI 27.8–62.5%). Transmission events tended to cluster by type of case: patientnoso were almost twice as likely to be infected by other patientnoso than expected (observed:expected ratio 1.91, 95%CrI 1.08 – 4.00, p = 0.02); similarly, HCWoutbreak were more than twice as likely to be infected by other HCWoutbreak than expected (2.25, 95%CrI 1.00–8.00, p = 0.04). The proportion of infectors of HCWcovid were as expected as random. The proportions of high transmitters (≥2 secondary cases) were significantly higher among HCWoutbreak than patientnoso in the late phases (26.2% vs. 13.4%, p<2.2e–16) of the outbreak. Conclusions Most importation events were linked to HCW. Unexpectedly, transmission between HCWcovid was more limited than transmission between patients and HCWoutbreak. This highlights gaps in infection control and suggests possible areas of improvements to limit the extent of nosocomial transmission.


2022 ◽  
Vol 2 ◽  
Author(s):  
Aurélien Madouasse ◽  
Mathilde Mercat ◽  
Annika van Roon ◽  
David Graham ◽  
Maria Guelbenzu ◽  
...  

2022 ◽  
Author(s):  
Miguel Ponce-de-Leon ◽  
Arnau Montagud ◽  
Vincent Noel ◽  
Gerard Pradas ◽  
Annika Meert ◽  
...  

Motivation: Cancer progression is a complex phenomenon that spans multiple scales from molecular to cellular and intercellular. Simulations can be used to perturb the underlying mechanisms of those systems and to generate hypotheses on novel therapies. We present a new version of PhysiBoSS, a multiscale modelling framework designed to cover multiple temporal and spatial scales, that improves its integration with PhysiCell, decoupling the cell agent simulations with the internal Boolean model in an easy-to-maintain computational framework. Results: PhysiBoSS 2.0 is a redesign and reimplementation of PhysiBoSS, conceived as an add-on that expands the PhysiCell agent-based functionalities with intracellular cell signalling using MaBoSS having a decoupled, maintainable and model-agnostic design. PhysiBoSS 2.0 successfully reproduces simulations reported in the former PhysiBoSS and expands its functionalities such as using user-defined models and cells' specifications, having mechanistic submodels of substrate internalisation with ODEs and enabling the study of drug synergies. Availability and implementation: PhysiBoSS 2.0 is open-source and publicly available on GitHub (https://github.com/PhysiBoSS/PhysiBoSS) under the BSD 3-clause license. Additionally, a nanoHUB tool has been set up to ease the use of PhysiBoSS 2.0 (https://nanohub.org/tools/pba4tnf/).


Molecules ◽  
2022 ◽  
Vol 27 (1) ◽  
pp. 292
Author(s):  
Timothy Bo Yuan Chen ◽  
Ivan Miguel De Cachinho Cordeiro ◽  
Anthony Chun Yin Yuen ◽  
Wei Yang ◽  
Qing Nian Chan ◽  
...  

Building polymers implemented into building panels and exterior façades have been determined as the major contributor to severe fire incidents, including the 2017 Grenfell Tower fire incident. To gain a deeper understanding of the pyrolysis process of these polymer composites, this work proposes a multi-scale modelling framework comprising of applying the kinetics parameters and detailed pyrolysis gas volatiles (parent combustion fuel and key precursor species) extracted from Molecular Dynamics models to a macro-scale Computational Fluid Dynamics fire model. The modelling framework was tested for pure and flame-retardant polyethylene systems. Based on the modelling results, the chemical distribution of the fully decomposed chemical compounds was realised for the selected polymers. Subsequently, the identified gas volatiles from solid to gas phases were applied as the parent fuel in the detailed chemical kinetics combustion model for enhanced predictions of toxic gas, charring, and smoke particulate predictions. The results demonstrate the potential application of the developed model in the simulation of different polymer materials without substantial prior knowledge of the thermal degradation properties from costly experiments.


OENO One ◽  
2022 ◽  
Vol 56 (1) ◽  
pp. 1-15
Author(s):  
Amber K. Parker ◽  
Jaco Fourie ◽  
Mike C. T. Trought ◽  
Kapila Phalawatta ◽  
Esther Meenken ◽  
...  

The time of flowering is key to understanding the development of grapevines. Flowering coincides with inflorescence initiation and fruit set, important determinants of yield. This research aimed to determine between and within-vine variability in 4-cane-pruned Sauvignon blanc inflorescence number per shoot, number of flowers per inflorescence and flowering progression using an objective method of assessing flowering via image capture and statistical analysis using a Bayesian modelling framework. The inflorescence number and number of flowers per inflorescence were measured by taking images over the flowering period. Flowering progression was assessed by counting open and closed flowers for each image over two seasons. An ordinal multinomial generalised linear mixed-effects model (GLMM) was fitted for inflorescence number, a Poisson GLMM for flower counts and a binomial GLMM for flowering progression. All the models were fitted and interpreted within a Bayesian modelling framework. Shoots arising from cane node one had lower numbers of inflorescences compared to those at nodes 3, 5 and 7, which were similar. The number of flowers per inflorescence was greater for basal inflorescences on a shoot than apical ones. Flowering was earlier, by two weeks, and faster in 2017/18 when compared to 2018/19 reflecting seasonal temperature differences. The time and duration of flowering varied at each inflorescence position along the cane. While basal inflorescences flowered later and apical earlier at lower insertion points on the shoot, the variability in flowering at each position on the vine dominated the date and duration of flowering.This is the first study using a Bayesian modelling framework to assess variability inflorescence presence and flower number, as well as flowering progression via objective quantification of open and closed flower counts rather than the more subjective method of visual estimation in the field or via cuttings. Although flower number differed for apical and basal bunches, little difference in timing and progression of flowering by these categories was observed. The node insertion point along a shoot was more important. Overall, the results indicate individual inflorescence variation and season are the key factors driving flowering variability and are most likely to impact fruit set and yield.


Author(s):  
Marios Prasinos ◽  
Ioannis Basdekis ◽  
Marco Anisetti ◽  
George Spanoudakis ◽  
Dimitris D.G Koutsouris ◽  
...  

Algorithms ◽  
2021 ◽  
Vol 15 (1) ◽  
pp. 16
Author(s):  
George Tzougas ◽  
Natalia Hong ◽  
Ryan Ho

In this article we present a class of mixed Poisson regression models with varying dispersion arising from non-conjugate to the Poisson mixing distributions for modelling overdispersed claim counts in non-life insurance. The proposed family of models combined with the adopted modelling framework can provide sufficient flexibility for dealing with different levels of overdispersion. For illustrative purposes, the Poisson-lognormal regression model with regression structures on both its mean and dispersion parameters is employed for modelling claim count data from a motor insurance portfolio. Maximum likelihood estimation is carried out via an expectation-maximization type algorithm, which is developed for the proposed family of models and is demonstrated to perform satisfactorily.


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