Integrating geostatistical maps and transmission models using adaptive multiple importance sampling

Retkute, Renata; Touloupou, Panayiota; Basáñez, María‐Gloria; Hollingsworth, T. Déirdre; Spencer, Simon E. F.

doi:10.1101/2020.08.03.20146241

Cited by 4 publications

(3 citation statements)

References 54 publications

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“…We further assumed that detectable individual CFUs are formed by either separated cells or these clusters. Parameter inference was performed using an adaptive multiple importance sampling framework [25]. The likelihood was obtained by assuming that the observed number of colonies is Poisson distributed:…”

Section: B Model For Plating With Glass Beadsmentioning

confidence: 99%

Effectiveness of glass beads for plating cell cultures

et al. 2021

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Cell plating, the spreading out of a liquid suspension of cells on a surface followed by colony growth, is a common laboratory procedure in microbiology. Despite this, the exact impact of its parameters on colony growth has not been extensively studied. A common protocol involves the shaking of glass beads within a Petri dish containing solid growth media. We investigated the effects of multiple parameters in this protocol: the number of beads, the shape of movement, and the number of movements. Standard suspensions of Escherichia coli were spread while varying these parameters to assess their impact on colony growth. Results were assessed by a variety of metrics: the number of colonies, the mean distance between closest colonies, and the variability and uniformity of their spatial distribution. Finally, we devised a mathematical model of shifting billiard to explain the heterogeneities in the observed spatial patterns. Exploring the parameters that affect the most fundamental techniques in microbiology allows us to better understand their function, giving us the ability to precisely control their outputs for our exact needs.

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Section: B Model For Plating With Glass Beadsmentioning

confidence: 99%

Effectiveness of glass beads for plating cell cultures

et al. 2021

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“…Parameter inference was performed using Adaptive Multiple Importance Sampling framework [25]. The likelihood was obtained by assuming that the observed number of colonies is Poisson-distributed: where Θ ={ n, r on , r off } ; n obs is the observed number of colonies; n sim is the number of colonies obtained after simulating the model with parameter set Θ.…”

Section: The Modelmentioning

confidence: 99%

The effectiveness of glass beads for plating cell cultures

Prusokas

Hawkins

Nieduszynski

et al. 2018

Preprint

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Cell plating and subsequent colony growth is an important laboratory procedure in microbiology. A common protocol for cell culture plating in Petri dishes uses glass beads to spread cells on the surface of the solid growth media. Here we perform an experimental analysis and mathematical modelling of cell plating. We introduce a new class of billiard -shifting billiard, which serves as a conceptual abstraction of the cell plating with glass beads. Numerical analysis of the dynamics of this simple yet efficient billiard, indicates a close relationship between plate movement and quality of colony distribution. Yeast Saccharomyces cerevisiae suspensions at different cell concentrations were used to confirm our theoretical observations.

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“…Therefore, models that account for people movements linked to spatial parasite transmission over large scales are needed. The ground-breaking recent work of Touloupou and Retkute, which links geostatistical mapping, a helminth transmission model and a statistical importance sampling method to produce very large-scale predictive maps, does include an element of spatial transmission, although does not incorporate observed people movement patterns [ 32 , 33 ].…”

Section: Introductionmentioning

confidence: 99%

How important is the spatial movement of people in attempts to eliminate the transmission of human helminth infections by mass drug administration?

Collyer,

Truscott,

Mwandawiro

et al. 2023

Phil. Trans. R. Soc. B

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Human mobility contributes to the spatial dynamics of many infectious diseases, and understanding these dynamics helps us to determine the most effective ways to intervene and plan surveillance. In this paper, we describe a novel transmission model for the spatial dynamics of hookworm, a parasitic worm which is a common infection across sub-Saharan Africa, East Asia and the Pacific islands. We fit our model, with and without mobility, to data obtained from a sub-county in Kenya, and validate the model's predictions against the decline in prevalence observed over the course of a clustered randomized control trial evaluating methods of administering mass chemotherapy. We find that our model which incorporates human mobility is able to reproduce the observed patterns in decline of prevalence during the TUMIKIA trial, and additionally, that the widespread bounce-back of infection may be possible over many years, depending on the rates of people movement between villages. The results have important implications for the design of mass chemotherapy programmes for the elimination of human helminth transmission. This article is part of the theme issue ‘Challenges and opportunities in the fight against neglected tropical diseases: a decade from the London Declaration on NTDs’.

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Integrating geostatistical maps and transmission models using adaptive multiple importance sampling

Cited by 4 publications

References 54 publications

Effectiveness of glass beads for plating cell cultures

Effectiveness of glass beads for plating cell cultures

The effectiveness of glass beads for plating cell cultures

How important is the spatial movement of people in attempts to eliminate the transmission of human helminth infections by mass drug administration?

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