http://hdl.handle.net/2117/3662 2013-05-19T20:51:19Z http://hdl.handle.net/2117/18453 Title: Explaining low farm-gate prices in the catalan wine sector: a Delphi study Authors: Costa Font, Montserrat; Serra Devesa, Teresa; Gil Roig, José María; Gras Moreu, Anna Maria 2013-03-21T12:59:31Z http://hdl.handle.net/2117/18009 Title: Modelización y simulación discreta con la plataforma NetLogo: ¿por qué caen las hojas en otoño? Authors: Ginovart Gisbert, Marta; Catalina, Merche; Blanco Abellán, Mónica Abstract: Los modelos basados en agentes (ABMs) describen a los individuos o partes que configuran un sistema como entidades autónomas y discretas, y focalizan toda su atención en caracterizar estas partes (agentes) mediante reglas de comportamiento, permitiendo la interacción entre ellas y con el entorno en el que se hallan. Se presenta el material docente diseñado para una actividad a realizar de forma autónoma en aula informática, centrada en el modelo “Autumn” que se encuentra en la plataforma NetLogo (de acceso libre desde la Web). Se analizan los resultados obtenidos con su implementación en los estudios de grado en Ingeniería de Biosistemas de la Universitat Politècnica de Catalunya. 2013-02-27T15:44:57Z http://hdl.handle.net/2117/17892 Title: Biochemical characterisation of minimally disturbed soils under mediterranean conditions. Authors: Jiménez de Ridder, Patrícia; Marando, Graciela; Josa March, Ramon; Julià Molí, Maria; Ginovart Gisbert, Marta; Bonmati Pont, Manuel 2013-02-20T09:06:41Z http://hdl.handle.net/2117/16652 Title: Discovering the power of agent-based modelling to deal with complex systems in diverse contexts Authors: Ginovart Gisbert, Marta; Portell Canal, Xavier; Blanco Abellán, Mónica Abstract: Modelling is a necessary tool to represent, analyse and discuss aspects or ideas related to complex systems. With this in mind, teaching science based on the elaboration of models is widely accepted in the academic community. A relatively new methodology of modelling exists with a different philosophy and perspective from the classic and continuous models used up usually, the so-called agent-based models (ABMs). The general aim of the work is to make this kind of discrete modelling well-known, so that ABMs may be incorporated progressively into the academic curricula, complementing other existing modelling strategies. 2012-10-05T09:35:29Z http://hdl.handle.net/2117/16232 Title: Low dose aerosol fitness at the innate phase of murine infection better predicts virulence amongst clinical strains of mycobacterium tuberculosis Authors: Cardona, Pere-Joan; Cáceres, Neus; Llopis Fuste, Isaac; Marzo, Elena; Prats Soler, Clara; Vilaplana, Cristina; García de Viedma, Darío; Samper, Sofia; López Codina, Daniel Abstract: Background: Evaluation of a quick and easy model to determine the intrinsic ability of clinical strains to generate active TB has been set by assuming that this is linked to the fitness of Mycobacterium tuberculosis strain at the innate phase of the infection. Thus, the higher the bacillary load, the greater the possibility of inducting liquefaction, and thus active TB, once the adaptive response is set. Methodology/Principal Findings: The virulence of seven clinical Mycobacterium tuberculosis strains isolated in Spain was tested by determining the bacillary concentration in the spleen and lung of mice at weeks 0, 1 and 2 after intravenous (IV) inoculation of 104 CFU, and by determining the growth in vitro until the stationary phase had been reached. Cord distribution automated analysis showed two clear patterns related to the high and low fitness in the lung after IV infection. This pattern was not seen in the in vitro fitness tests, which clearly favored the reference strain (H37Rv). Subsequent determination using a more physiological low-dose aerosol (AER) inoculation with 102 CFU showed a third pattern in which the three best values coincided with the highest dissemination capacity according to epidemiological data. Conclusions/Significance: The fitness obtained after low dose aerosol administration in the presence of the innate immune response is the most predictive factor for determining the virulence of clinical strains. This gives support to a mechanism of the induction of active TB derived from the dynamic hypothesis of latent tuberculosis infection. 2012-07-11T12:56:31Z http://hdl.handle.net/2117/15579 Title: Biochemical characterisation of minimally disturbed soils under mediterranean conditions Authors: Jiménez de Ridder, Patrícia; Marando, Graciela; Josa March, Ramon; Julià Molí, Maria; Ginovart Gisbert, Marta; Bonmati Pont, Manuel 2012-03-15T09:54:44Z http://hdl.handle.net/2117/14135 Title: Upgrading the uptake and metabolism sub-models of the Individual-based Model INDISIM-YEAST to tackle the behaviour of Saccharomyces cerevisiae in different culture conditions Authors: Portell Canal, Xavier; Gras Moreu, Anna Maria; Carbó Moliner, Rosa; Ginovart Gisbert, Marta 2011-12-01T12:27:02Z http://hdl.handle.net/2117/13753 Title: Optimization methods for individual-based model parameter estimation in predictive microbiology Authors: Prats Soler, Clara; Bernaerts, K.; Standaert, A.; Ferrer Savall, Jordi; López Codina, Daniel; Van Impe, J. Abstract: In the framework of microbiology, Individual-based Models are discrete models in which the main entities are microbes. Their use in simulations as ‘virtual experiments’ to predict the evolution of populations under specific conditions requires accurate setting of the parameters involved. We adapted and tested two optimization methods for Individual-based Model parameter estimation: the Nelder-Mead Threshold Accepting (NMTA) and the NEWUOA. These methods presented no convergence problems, and the best results in terms of time expenditure were derived with the latter. 2011-11-07T10:23:12Z http://hdl.handle.net/2117/13742 Title: Thermodynamic concepts in the study of microbial populations: age structure in plasmodium falciparum infected red blood cells Authors: Ferrer Savall, Jordi; Prats Soler, Clara; López Codina, Daniel; Vidal-Mas, Jaume; Gargallo-Viola, Domingo; Guglietta, Antonio; Giró Roca, Antoni Abstract: Variability is a hallmark of microbial systems. On the one hand, microbes are subject to environmental heterogeneity and undergo changeable conditions in their immediate surroundings. On the other hand, microbial populations exhibit high cellular diversity. The relation between microbial diversity and variability of population dynamics is difficult to assess. This connection can be quantitatively studied from a perspective that combines in silico models and thermodynamic methods and interpretations. The infection process of Plasmodium falciparum parasitizing human red blood cells under laboratory cultivation conditions is used to illustrate the potential of Individual-based models in the context of predictive microbiology and parasitology. Experimental data from several in vitro cultures are compared to the outcome of an individual-based model and analysed from a thermodynamic perspective. This approach allows distinguishing between intrinsic and external constraints that give rise to the diversity in the infection forms, and it provides a criterion to quantitatively define transient and stationary regimes in the culture. Increasing the ability of models to discriminate between different states of microbial populations enhances their predictive capability which finally leads to a better the control over culture systems. The strategy here presented is of general application and it can substantially improve modelling of other types of microbial communities. 2011-11-06T16:13:32Z http://hdl.handle.net/2117/13553 Title: Modelos basados en el individuo y la plataforma NetLogo Authors: Ginovart Gisbert, Marta; Portell Canal, Xavier; Ferrer-Closas, Pol; Blanco Abellán, Mónica Abstract: El objetivo general de este trabajo se enmarca en el deseo de dar a conocer la metodología de la modelización basada en el individuo y sus posibilidades para ser utilizada, entre otras metodologías, en la adquisición de la competencia de modelización en docencia. Para ello se presenta: i) una descripción de los elementos que permiten identificar, describir, comunicar e implementar los modelos basados en el individuo (IBMs), y como obtener resultados de simulación; y ii) un ejemplo-muestra de un IBM de NetLogo que ilustra con detalle la manera de proceder con este tipo de modelo 2011-10-17T17:56:32Z http://hdl.handle.net/2117/13546 Title: Microbial individual-based models and sensitivity analyses: local and global methods Authors: Ginovart Gisbert, Marta; Prats Soler, Clara; Portell Canal, Xavier Abstract: A microbial Individual-based Model (IbM) to deal with yeast populations growing in liquid batch cultures has been designed and implemented in a simulator called INDISIM-YEAST. Interesting qualitative results have already been achieved with its use in the study of fermentation profiles, small inocula dynamics and lag phase, among others. Nevertheless, in order to improve its predictive capabilities and further development, a deeper comprehension of how the variation of the output of the model can be apportioned to different sources of variation must be investigated. One way to consider a sensitivity analysis for this IbM, providing an understanding of how the model response variables react to changes in the inputs, is the statistical study of well-designed computer experiments. The aim of this contribution is to show how the insights into nine individual cell parameters of INDISIMYEAST, mainly related to uptake and reproduction sub-models, can be obtained by combining local and global sensitivity analyses using simple and classic methods. From data obtained with an extensive set of computer experiments, a study of the variability observed in the evolution of two outputs of this model, ethanol production and mean biomass of the population, was performed. In addition, mono-factorial (one-at-a-time) analyses and ANOVA-based global analyses were also carried out on these two outputs. The model is clearly less sensitive to some parameters than others, depending on the output controlled. Moreover, this study allows identification of the parameters which have the greatest impact on the corresponding outputs and their significant first-order interactions. This work must be understood as an exercise to set up the procedure to be used in a sensitivity analysis study involving microbial IbMs. The knowledge gained will facilitate future parameterization and calibration of different parameters and outputs depending on the purpose of any study. 2011-10-17T14:41:30Z http://hdl.handle.net/2117/13510 Title: Sensitivity analysis and individual-based models in the study of yeast populations Authors: Ginovart Gisbert, Marta; Prats Soler, Clara; Portell Canal, Xavier Abstract: Individual-based models (IBMs), the biological agent-based models, are currently being applied to the study of microbial systems. A microbial IBM of yeast populations growing in liquid bath cultures has already been designed and implemented in the simulator called INDISIM-YEAST. In order to improve its predictive capabilities and further its development, a deeper understanding of how the variation of the output of the model can be apportioned, qualitatively or quantitatively, to different sources of variation must be investigated. The aim of this study is to show how insights into the individual cell parameters of INDISIM-YEAST can be obtained combining local and global methods using classic and well-proven methods, and to illustrate how these simple methods provide useful, reliable results with this IBM. This work deals mainly with the use of screening methods, as the main task to perform here is that of identifying the most influential factors for this microbial IBM. This screening exercise has allowed the establishment of significant input factors to this IBM on yeast population growth, and the highlighting of those that require greater attention in the parameterization and calibration processes. 2011-10-14T12:53:24Z http://hdl.handle.net/2117/13098 Title: Effect of environmental fluctuations on invasion fronts Authors: Mendez, Vicenç; Llopis Fuste, Isaac; Campos, Daniel; Horsthemke, Werner Abstract: We determine the density profile and velocity of invasion fronts in one-dimensional infinite habitats in the presence of environmental fluctuations. The population dynamics is reformulated in terms of a stochastic reaction–diffusion equation and is reduced to a deterministic equation that incorporates the systematic contributions of the noise. We obtain analytical expressions for the front profile and velocity by constructing a variational principle. The effect of the noise differs, depending on whether it affects the density-independent growth rate, the intraspecific competition term or the Allee threshold. Fluctuations in the density-independent growth rate increase the invasion velocity and the population density of the invaded area. Fluctuations in the competition term also change the population density of the invaded area, but modify the invasion velocity only for certain initial conditions. Fluctuations in the Allee threshold can induce pulled or pushed invasion fronts as well as invasion failure. We compare our analytical results with numerical solutions of the stochastic partial differential equations and show that our procedure proves useful in dealing with reaction–diffusion equations with multiplicative noise. 2011-08-24T08:31:56Z http://hdl.handle.net/2117/13096 Title: Extinction conditions for isolated populations with Allee effect Authors: Mendez, Vicenç; Sans, Cristina; Llopis Fuste, Isaac; Campos, Daniel Abstract: One of the main ecological phenomenons is the Allee effect, in which a positive benefit from the presence of conspecifics arises. In this work we describe the dynamical behavior of a population with Allee effect in a finite domain that is surrounded by a completely hostile environment. Using spectral methods to rewrite the local density of habitants we are able to determine the critical patch size and the bifurcation diagram, hence characterizing the stability of possible solutions, for different ways to introduce the Allee effect in the reaction–diffusion equations. 2011-08-23T10:58:11Z http://hdl.handle.net/2117/12708 Title: Exploring the lag phase and growth initiation of a yeast culture by means of an individual-based model Authors: Ginovart Gisbert, Marta; Prats Soler, Clara; Portell Canal, Xavier; Silbert, Moises Abstract: The performance of fermentation processes is greatly influenced by the size and quality of inocula. The characterization of the replicative age is decided by the number of birth scars each yeast exhibits on its cellular membrane. Yeast ageing and inoculum size are factors that affect industrial fermentation, particularly those processes in which the yeast cells are reused such as the production of beer. This process reuses yeast cropped at the end of one fermentation in the following one, in a process called “serial repitching”. The aim of this study was to explore the effects of inoculum size and ageing on the first stages of the dynamics of yeast population growth. However, only Individual-based Models (IbMs) allow the study of small, well-characterized, microbial inocula. We used INDISIM-YEAST, based on the generic IbM simulator INDISIM, to carry out these studies. Several simulations were performed to analyze the effect of the inoculum size and genealogical age of the cells that made it up on the lag phase, first division time and specific growth rate. The shortest lag phase and time to the first division were obtained with largest inocula and with the youngest inoculated parent cells. Keywords: Individual-based model; Lag phase; Growth initiation; Yeast inoculum; Inoculum size; Yeast cell age. 2011-06-03T14:56:40Z