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Surrogate-based uncertainty and sensitivity analysis for bacterial invasion in multi-species biofilm modeling

A. Trucchia, M.R. Mattei, V. Luongo, L. Frunzo, M.C. Rochoux
2019 Communications in nonlinear science & numerical simulation  
In this work, we present a probabilistic analysis of a detailed one-dimensional biofilm model that explicitly accounts for planktonic bacterial invasion in a multi-species biofilm.  ...  bacterial invasion as described by a recent multi-species biofilm model 115 and use it to perform uncertainty quantification and global sensitivity analy-116 sis.  ...  work, uncertainty quantification and global sensitivity analysis 720 non-intrusive methods were applied to a novel and promising multi-species 721 microbial biofilm model, which explicitly accounts for  ... 
doi:10.1016/j.cnsns.2019.02.024 fatcat:i2ylyaveibg35ddylwn3edalsq

Gaussian process emulation of an individual-based model simulation of microbial communities

O.K. Oyebamiji, D.J. Wilkinson, P.G. Jayathilake, T.P. Curtis, S.P. Rushton, B. Li, P. Gupta
2017 Journal of Computational Science  
Our aim in this paper is to build a cheaper surrogate of an individual-based (IB) model simulation of microbial communities.  ...  Under cross-validation, the percentage of variance explained for the univariate emulator ranges from 83-99% and 87-99% for the multivariate emulators, and for both biofilms and floc.  ...  EP/K039083/1), by the Newcastle University Frontiers in Engineering Biology (NUFEB) project. We thank the NUFEB modelling team for their useful comments that have helped improve this paper.  ... 
doi:10.1016/j.jocs.2017.08.006 fatcat:7r7yyzzwzzh5fgb3lvlubaipuu

A Bayesian approach to modelling the impact of hydrodynamic shear stress on biofilm deformation

Oluwole K. Oyebamiji, Darren J. Wilkinson, Pahala Gedara Jayathilake, Steve P. Rushton, Ben Bridgens, Bowen Li, Paolo Zuliani, Robert Nerenberg
2018 PLoS ONE  
We investigate the feasibility of using a surrogate-based method to emulate the deformation and detachment behaviour of a biofilm in response to hydrodynamic shear stress.  ...  The surrogate models are shown to perform well, and produced % 480 fold increase in computational efficiency.  ...  Acknowledgments We thank the NUFEB modelling team for their useful comments that have helped improve this paper. Author Contributions Conceptualization: Oluwole K. Oyebamiji, Steve P.  ... 
doi:10.1371/journal.pone.0195484 pmid:29649240 pmcid:PMC5896950 fatcat:hqdofgn2gvakvfpxo2usk5nfoi

Overcoming antifungal resistance

Anand Srinivasan, Jose L. Lopez-Ribot, Anand K. Ramasubramanian
2014 Drug Discovery Today : Technologies  
Fungal infections have become one of the major causes of morbidity and mortality in immunocompromised patients.  ...  In this review, we will discuss the advent of cellular-microarrays, microfluidics, genomics, proteomics and other state-of-the art technologies in conquering antifungal drug resistance.  ...  Acknowledgments Work in the laboratory is funded by Grants numbered SC1HL112629 (to A.K.R) and R01DE023510 (to J.L.L.  ... 
doi:10.1016/j.ddtec.2014.02.005 pmid:24847655 pmcid:PMC4031462 fatcat:vk6uniwl4rcifhcbt3zwsxkwlu


Isabel Muñoz Gracia, Sergi Sabater
2013 Acta Biológica Colombiana  
ABSTRACT This paper describes various approaches to evaluating ecological risk in rivers affected by multiple chemical stressors, with emphasis on biofilm and invertebrate community responses.  ...  Weight of evidence is an integrative methodology for tackling the challenge of determining causal relations and applying this knowledge in the decision-making processes of river management.  ...  ACKNOWLEDGEMENTS This research was funded by the Spanish Ministry of Economy and Competitiveness SCARCE project (Consolider-Ingenio 2010 program, project: CSD2009-00065).  ... 
doi:10.15446/abc.v19n1.38461 fatcat:qdzqjxrsavcnxfptdoxnskgryu

Recent trends in molecular diagnostics of yeast infections: from PCR to NGS

2019 FEMS Microbiology Reviews  
Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis.  ...  These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection.  ...  Recently, an LFD for detection of human host antibodies against C. albicans enolase as a surrogate marker for invasive candidiasis in serum samples has been described.  ... 
doi:10.1093/femsre/fuz015 pmid:31158289 pmcid:PMC8038933 fatcat:yzoham6uzja3jdwqwvck3oiqkm

ICPMF 10 proceedings

Fernando Perez-Rodriguez
2021 Zenodo  
Proceedings of 10th International Conference on Predictive Modelling in Food held in Cordoba (Spain) from 26 to 29 of September 2017  ...  Naouel Boussoualim University of Setif, Setif, Argelia Keywords: Flavonoids and Polyphenols, Antibiotics, Synergy, Antibacterial activity  ...  A sensitivity analysis was conducted to quantify the influence of the uncertainty due to the inputs on the model output.  ... 
doi:10.5281/zenodo.5093829 fatcat:bzpnf3dv2nhntdkvhzijjpaeje

Oral presentations

2007 Clinical Microbiology and Infection  
Bacterial identification was performed by both standard biochemical profiles and amplification of species specific genes.  ...  Analysis of trends used mean S rates by nation for the initial and last 3 years sampled.  ...  No difference was found between species in biofilm development.  ... 
doi:10.1111/j.1469-0691.2007.01732.x pmid:17391428 pmcid:PMC7129154 fatcat:dznj72ssubd3fpoxhfcwx6c2mi

Oral presentations

2009 Clinical Microbiology and Infection  
The bacterial pathogen Listeria monocytogenes: a multi-faceted model K170 Listeria monocytogenes: a bacterial pathogen responsible for severe infections and a multi-faceted model in biology P.  ...  Bayesian Model Averaging was used to account for model uncertainty. Results: Before the interventions the use of QUIN (both iv and total) was stable.  ...  Positive blood culture for CRAB remained in the final model (HR 1.85; 95% CI 0.86−4.00; p = 0.12). All 25 isolates submitted to PCR were positive for blaoxa-23.  ... 
doi:10.1111/j.1469-0691.2009.02857.x pmid:19519682 pmcid:PMC7162236 fatcat:vpyx2lglbjgcjm2fcs7bf4x6pi

Common principles and best practices for engineering microbiomes

Christopher E. Lawson, William R. Harcombe, Roland Hatzenpichler, Stephen R. Lindemann, Frank E. Löffler, Michelle A. O'Malley, Héctor García Martín, Brian F. Pfleger, Lutgarde Raskin, Ophelia S. Venturelli, David G. Weissbrodt, Daniel R. Noguera (+1 others)
2019 Nature Reviews Microbiology  
Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges.  ...  In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled  ...  2018, which all authors attended and at which all authors participated in discussions that led to the creation of this article.  ... 
doi:10.1038/s41579-019-0255-9 pmid:31548653 pmcid:PMC8323346 fatcat:33lo56levzhahan3y3shhiselm

Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges

Lucie Collineau, Patrick Boerlin, Carolee A. Carson, Brennan Chapman, Aamir Fazil, Benjamin Hetman, Scott A. McEwen, E. Jane Parmley, Richard J. Reid-Smith, Eduardo N. Taboada, Ben A. Smith
2019 Frontiers in Microbiology  
This review explores opportunities and challenges of integrating WGS data into QMRA models that follow the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR.  ...  We strongly recommend that methodologies to incorporate WGS data in risk assessment be included in any future revision of the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR.  ...  Sensitivity analysis should also be conducted to identify those parameters having the largest influence on the model outcomes.  ... 
doi:10.3389/fmicb.2019.01107 pmid:31231317 pmcid:PMC6558386 fatcat:pexfrx3xzrholfapjiumplnoma

Volume 42 Number 2

2021 Microbiology Australia  
We encourage and welcome your engagement using any option that suits you.  ...  To join the ASM community, go to and click on the icon at the top RHS of the screen to set up your profile.  ...  (b) Fluorescence in situ hybridisation on the same middle ear effusion demonstrating multi-species bacterial biofilms using the following 16s rRNA probes: universal bacterial probe (red), S. pneumoniae  ... 
doi:10.1071/mav42n2 fatcat:b53wgaah3reh7cdsvghn336xwi

Heterotrophic Plate Counts and Drinking-water Safety: The Significance of HPCs for Water Quality and Human Health

J. Bartram
2013 Water Intelligence Online  
when lactose-based media are employed and as HPC is a surrogate indicator for chlorine residuals in distribution systems.  ...  In the absence of biofilm pathogen testing protocols, surrogates that indicate biofilm development -and therefore potential for increased health risk -have been instigated for some time and include deteriorating  ...  92 animal model systems, autochthonous bacteria health risk assessment 0 antibody-based methods 53-4 AOC level see assimilable organic carbon arbitrarily primed PCR (AP-PCR) 62-3 Asellus 204 Aspergillus  ... 
doi:10.2166/9781780405940 fatcat:cmwvtupohjcbhicifip4fsshya

Oral presentations

2011 Clinical Microbiology and Infection  
Results: AcrB and TolC mutants both formed much less biofilm than wildtype in the simple 'crystal violet' biofilm model and mutants formed no biofilm in the more complex 'biofilm mat' model in comparison  ...  The same isolates were then tested in a biofilm model. Biofilm sampling was done and the MBC's for polymyxin B and rifampin were determined.  ...  The semi-quantative culture was used for identification of different bacterial species and the pyrosequencing-based method was used for detection of TLR4 polymorphism Asp299Gly. and GS13TU isolates were  ... 
doi:10.1111/j.1469-0691.2011.03557.x fatcat:hgjyme5qh5fgplu5nk32hbf7tm

Oral presentations

2008 Clinical Microbiology and Infection  
Therefore, knowledge of surrogate organisms for the analysis of patient-to-patient transmissions would be useful.  ...  Conclusions: Pneumococcal biofilm formation can be assayed in different systems which provide alternative models for the analysis of this complex phenotype.  ...  Results: A total of 174 patients switched ARV regimen to NVP-based regimen and 162 patients had available data for further analysis.  ... 
doi:10.1111/j.1469-0691.2008.02006.x pmid:18399911 pmcid:PMC7129943 fatcat:tbctrv2iwfc45dc4oxavr4crla
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