Bayesian hierarchical modelling of bacteria growth

Bacterial growth models are commonly used in food safety. Such models permit the prediction of microbial safety and the shelf life of perishable foods. In this paper, we study the problem of modelling bacterial growth when we observe multiple experimental results under identical environmental conditions. We develop a hierarchical version of the Gompertz equation to take into account the possibility of replicated experiments and we show how it can be fitted using a fully Bayesian approach. This approach is illustrated using experimental data from Listeria monocytogenes growth and the results are compared with alternative models. Model selection is undertaken throughout using an appropriate version of the deviance information criterion and the posterior predictive loss criterion. Models are fitted using WinBUGS via R2WinBUGS.Predictive microbiology, Growth models, Gompertz curve, Bayesian hierarchical modelling

Pattern formation and optimization in army ant raids

Army ant colonies display complex foraging raid patterns involving thousands of individuals communicating through chemical trails. In this paper we explore, by means of a simple search algorithm, the properties of these trails in order to test the hypothesis that their structure reflects an optimized mechanism for exploring and exploiting food resources. The raid patterns of three army ant species, {em Eciton hamatum}, {em Eciton burchelli} and {em Eciton rapax}, are analysed. The respective diets of these species involve large but rare, small but common, and a combination of large but rare and small but common, food sources. Using a model proposed by Deneubourg and collaborators, we simulate the formation of raid patterns in response to different food distributions. Our results indicate that the empirically observed raid patterns maximise return on investment, that is, the amount of food brought back to the nest per unit of energy expended, for each of the diets. Moreover, the values of the parameters that characterise the three optimal pattern-generating mechanisms are strikingly similar. Therefore the same behavioural rules at the individual level can produce optimal colony-level patterns. The evolutionary implications of these findings are discussed.Postprint (published version

Initiating Change of People With Criminal Justice Involvement Through Participation in a Drama Project: An Exploratory Study

Introduction: Innovative and interdisciplinary approaches are needed to improve mental health and psychosocial outcomes of people with criminal justice involvement and their families. Aim of the study was to assess effects of the participation in a theatre project on the mental health problems of people with criminal justice involvement and relatives. Methods: We conducted structured diagnostic interviews and in-depth qualitative interviews with five participants performing Shakespeare's Richard III in Chile. Three participants had been imprisoned prior to the project, and two were the parents of a person who died in a prison fire. Qualitative interviews followed a topic guide. Data were transcribed, and a six-phase approach for thematic analysis of the data was used. Results: Substance use disorder or major depression was identified in all the participants. Participation in the theatre project was experienced by the respondents as having a positive effect on the mental health conditions. The research registered the positive experiences of role identification, emotional expression, commitment with group processes, improved skills to socially interact, to be heard by the general public and society, and positive perceptions of the audience (including relatives). Discussion: The study raises the possibility that there may be improvements of depression and substance use problems through the participation of people with criminal justice involvement in a drama project. Wider scale research is recommended on the possible effects. The approach may be an alternative to psychotherapy and medication for some individuals

Photonic heterostructures with Levy-type disorder: statistics of coherent transmission

We study the electromagnetic transmission $T$ through one-dimensional (1D) photonic heterostructures whose random layer thicknesses follow a long-tailed distribution --L\'evy-type distribution. Based on recent predictions made for 1D coherent transport with L\'evy-type disorder, we show numerically that for a system of length $L$ (i) the average $\propto L^\alpha$ for $0 \propto L$ for $1\le\alpha<2$, $\alpha$ being the exponent of the power-law decay of the layer-thickness probability distribution; and (ii) the transmission distribution $P(T)$ is independent of the angle of incidence and frequency of the electromagnetic wave, but it is fully determined by the values of $\alpha$ and $$.Comment: 4 pages, 4 figure

Explaining the visible and the invisible: Public knowledge of genetics, ancestry, physical appearance and race in Colombia

This is the final version of the article. Available from SAGE Publications via the DOI in this record.Using data from focus groups conducted in Colombia, we explore how educated lay audiences faced with scenarios about ancestry and genetics draw on widespread and dominant notions of nation, race and belonging in Colombia to ascribe ancestry to collectivities and to themselves as individuals. People from a life sciences background tend to deploy idioms of race and genetics more readily than people from a humanities and race-critical background. When they considered individuals, people tempered or domesticated the more mechanistic explanations about racialized physical appearance, ancestry and genetics that were apparent at the collective level. Ideas of the latency and manifestation of invisible traits were an aspect of this domestication. People ceded ultimate authority to genetic science, but deployed it to work alongside what they already knew. Notions of genetic essentialism co-exist with the strategic use of genetic ancestry in ways that both fix and unfix race. Our data indicate the importance of attending to the different epistemological stances through which people define authoritative knowledge and to the importance of distinguishing the scale of resolution at which the question of diversity is being posed.This article arises out of two projects: ‘Race, genomics and mestizaje (mixture) in Latin America: a comparative approach’ funded by the Economic and Social Research Council (ESRC) (grant RES-062-23-1914) and ‘Public engagement with genomic research and race in Latin America’ funded by The Leverhulme Trust (grant RPG-044)

Stationary and moving breathers in a simplified model of curved alpha--helix proteins

The existence, stability and movability of breathers in a model for alpha-helix proteins is studied. This model basically consists a chain of dipole moments parallel to it. The existence of localized linear modes brings about that the system has a characteristic frequency, which depends on the curvature of the chain. Hard breathers are stable, while soft ones experiment subharmonic instabilities that preserve, however the localization. Moving breathers can travel across the bending point for small curvature and are reflected when it is increased. No trapping of breathers takes place.Comment: 19 pages, 11 figure

Modelado del juego de la cerveza mediante simulación basada en agentes usando PECS

El juego de la cerveza ha sido ampliamente estudiado y tradicionalmente ha sido modelado usando dinámica de sistemas. Hasta el momento no existen trabajos que estudien la dinámica del juego desde la perspectiva del comportamiento humano, además el nivel de agregación usado en dinámica de sistemas no permite estudiar el efecto de las características propias de cada individuo en la dinámica del comportamiento del juego. Por tal razón, el principal propósito de éste trabajo versa sobre el efecto que tiene incluir el comportamiento individual de los agentes que participan en el juego de la cerveza, en la dinámica del mismo. Con este objetivo se desarrolla un modelo de simulación basado en agentes que incorpora la plataforma PECS, por medio de dicha plataforma es que se logra incorporar el modelado del comportamiento humano en el modelo de simulación del juego. Los resultados de la simulación sugieren que la incorporación de factores humanos en el juego, no altera la dinámica del mismo, sin embargo, permite identificar y estudiar las emociones que causan las decisiones de los jugadores, que en general tienden a estar bastante alejadas de las decisiones óptimas.The beer game has been widely studied and traditionally has been modeled using systems dy-namics. To date, there is no evidence of studies of the game’s dynamics from the human behavior perspective. In addition, the aggregation level used in systems dynamics does not let studying the effect of the individuals’ characteristics in the game’s dynamics. That is why the main pur-pose of this paper is to analyze the consequences of introducing the self-behavior of the agents who participate in the beer game, on its own dynamics. Pursuing this objective, an agent based model which incorporates PECS framework is developed. This framework is responsible for articulating the human behavior model inside the agent based simulation model. The results of the simulation show that considering human factors into the model of the game, does not alter its dynamics. Nevertheless, it permits identifying and studying the emotions that cause the different decisions of the players, that in general terms tend to be significantly far from the optimal decisions