Half a billion simulations: evolutionary algorithms and distributed computing for calibrating the SimpopLocal geographical model

Multi-agent geographical models integrate very large numbers of spatial interactions. In order to validate those models large amount of computing is necessary for their simulation and calibration. Here a new data processing chain including an automated calibration procedure is experimented on a computational grid using evolutionary algorithms. This is applied for the first time to a geographical model designed to simulate the evolution of an early urban settlement system. The method enables us to reduce the computing time and provides robust results. Using this method, we identify several parameter settings that minimise three objective functions that quantify how closely the model results match a reference pattern. As the values of each parameter in different settings are very close, this estimation considerably reduces the initial possible domain of variation of the parameters. The model is thus a useful tool for further multiple applications on empirical historical situations

A modular modelling framework for hypotheses testing in the simulation of urbanisation

In this paper, we present a modelling experiment developed to study systems of cities and processes of urbanisation in large territories over long time spans. Building on geographical theories of urban evolution, we rely on agent-based models to 1/ formalise complementary and alternative hypotheses of urbanisation and 2/ explore their ability to simulate observed patterns in a virtual laboratory. The paper is therefore divided into two sections : an overview of the mechanisms implemented to represent competing hypotheses used to simulate urban evolution; and an evaluation of the resulting model structures in their ability to simulate - efficiently and parsimoniously - a system of cities (the Former Soviet Union) over several periods of time (before and after the crash of the USSR). We do so using a modular framework of model-building and evolutionary algorithms for the calibration of several model structures. This project aims at tackling equifinality in systems dynamics by confronting different mechanisms with similar evaluation criteria. It enables the identification of the best-performing models with respect to the chosen criteria by scanning automatically the parameter along with the space of model structures (as combinations of modelled dynamics).Comment: 21 pages, 3 figures, working pape

OpenMOLE, a workflow engine specifically tailored for the distributed exploration of simulation models

International audienceComplex-systems describe multiple levels of collective structure and organization. In such systems, the emergence of global behaviour from local interactions is generally studied through large scale experiments on numerical models. This analysis generates important computation loads which require the use of multi-core servers, clusters or grid computing. Dealing with such large scale executions is especially challenging for modellers who don't possess the theoretical and methodological skills required to take advantage of high performance computing environments. That's why we have designed a cloud approach for model experimentation. This approach has been implemented in OpenMOLE (Open MOdel Experiment) as a Domain Specific Language (DSL) that leverages the naturally parallel aspect of model experiments. The OpenMOLE DSL has been designed to explore user-supplied models. It delegates transparently their numerous executions to remote execution environment. From a user perspective, those environments are viewed as services providing computing power, therefore no technical detail is ever exposed. This paper presents the OpenMOLE DSL through the example of a toy model exploration and through the automated calibration of a real-world complex system model in the field of geography

L’enjeu de la rédaction professionnelle au XXIème siècle. : des outils pluridisciplinaires au service d’une écriture de haut niveau

International audienceL'enjeu de la rédaction professionnelle au XXIème siècle : des outils pluridisciplinaires au service d'une écriture de haut niveau Cet article est pour nous l'occasion de questionner l'acte d'écrire du rédacteur professionnel à travers la discipline linguistique. Notre analyse vise à montrer que le savoir-faire en écriture du Rédacteur Professionnel requiert des compétences dans le code écrit mais révèle aussi des compétences en écriture de haut niveau et de communication (Clerc & Beaudet, 2008 ; Labasse, 2008). Par analogie aux travaux sur la lecture distinguant une lecture analytique d'une lecture globale, nous émettons l'hypothèse que le savoir-faire d'un expert en écriture professionnelle porte sur sa capacité à articuler écriture analytique (en tant que maîtrise du code linguistique dans sa complexité) et écriture globale (en tant que maîtrise de la situation de communication, de la gestion de la relation, et finalement d'efficacité du message transmis). Le maniement des unités graphiques et l'ordonnancement de ces unités au sein des séquences textuelles doivent donc se réaliser à l'intérieur d'une écriture globale intégrant les éléments de dénotation et de connotation des co-énonciateurs. Si cela est validé, nous nous inscrirons dans la lignée des travaux confrontant la pratique de la rédaction professionnelle à son « efficacité interactionnelle » (Clerc & Beaudet, 2008 ; Romain, Rey & Pereira, 2013). Nous nous intéressons à l'étude de la production de ces écrits sous deux angles complémentaires :-l'écriture analytique, c'est-à-dire l'écriture communicante qui gère l'information pure (convocation du code linguistique dans sa complexité), l'objectif étant d'être efficace dans la transmission de l'information ;-l'écriture globale, c'est-à-dire l'énonciation de textes favorisant une forme de co-gestion de la communication, afin que le texte soit lu avec une efficacité relationnell

Individual motile CD4+ T cells can participate in efficient multikilling through conjugation to multiple tumor cells

T cells genetically modified to express a CD19-specific chimeric antigen receptor (CAR) for the investigational treatment of B-cell malignancies comprise a heterogeneous population, and their ability to persist and participate in serial killing of tumor cells is a predictor of therapeutic success. We implemented Timelapse Imaging Microscopy in Nanowell Grids (TIMING) to provide direct evidence that CD4+CAR+ T cells (CAR4 cells) can engage in multikilling via simultaneous conjugation to multiple tumor cells. Comparisons of the CAR4 cells and CD8+CAR+ T cells (CAR8 cells) demonstrate that, although CAR4 cells can participate in killing and multikilling, they do so at slower rates, likely due to the lower granzyme B content. Significantly, in both sets of T cells, a minor subpopulation of individual T cells identified by their high motility demonstrated efficient killing of single tumor cells. A comparison of the multikiller and single-killer CAR+ T cells revealed that the propensity and kinetics of T-cell apoptosis were modulated by the number of functional conjugations. T cells underwent rapid apoptosis, and at higher frequencies, when conjugated to single tumor cells in isolation, and this effect was more pronounced on CAR8 cells. Our results suggest that the ability of CAR+ T cells to participate in multikilling should be evaluated in the context of their ability to resist activation-induced cell death. We anticipate that TIMING may be used to rapidly determine the potency of T-cell populations and may facilitate the design and manufacture of next-generation CAR+ T cells with improved efficacy. Cancer Immunol Res; 3(5); 473–82. ©2015 AACR

Network analysis of the associations between personality traits, cognitive functioning, and inflammatory markers in elderly individuals without dementia

IntroductionLower cognitive functioning in old age has been associated with personality traits or systemic inflammatory markers. Associations have also been found between personality traits and inflammatory markers. However, no study has explored the inter-relationships between these three components simultaneously. The present study aims to better understand the inter-relationships among personality traits, inflammatory markers, and cognitive performance in elderly individuals without dementia.MethodsThis study utilizes a network analysis approach, a statistical method that allows visualization of the data’s unique pairwise associations. We performed a cross-sectional analysis on 720 elderly individuals without dementia, using data from Colaus|PsyColaus, a population-based study conducted in Lausanne, Switzerland. The Revised NEO Five-Factor Inventory (NEO-FFI-R) was used to assess personality traits, and interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), and C-reactive protein (CRP) were used as peripheral inflammatory markers. Cognitive domains were investigated using the Mini-Mental State Examination (MMSE), the Verbal Fluency Test, the Stroop Test, the DO40, and the Free and Cued Selective Reminding (FCSR) test.ResultsOpenness was associated with verbal fluency and Agreeableness with immediate free recall. In contrast, no association between inflammatory markers and personality traits or cognition was identified.DiscussionIn elderly individuals without dementia, a high level of Openness or Agreeableness was associated with executive functioning/semantic memory and episodic memory, respectively

Front Aging Neurosci

INTRODUCTION: Lower cognitive functioning in old age has been associated with personality traits or systemic inflammatory markers. Associations have also been found between personality traits and inflammatory markers. However, no study has explored the inter-relationships between these three components simultaneously. The present study aims to better understand the inter-relationships among personality traits, inflammatory markers, and cognitive performance in elderly individuals without dementia. METHODS: This study utilizes a network analysis approach, a statistical method that allows visualization of the data's unique pairwise associations. We performed a cross-sectional analysis on 720 elderly individuals without dementia, using data from Colaus|PsyColaus, a population-based study conducted in Lausanne, Switzerland. The Revised NEO Five-Factor Inventory (NEO-FFI-R) was used to assess personality traits, and interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), and C-reactive protein (CRP) were used as peripheral inflammatory markers. Cognitive domains were investigated using the Mini-Mental State Examination (MMSE), the Verbal Fluency Test, the Stroop Test, the DO40, and the Free and Cued Selective Reminding (FCSR) test. RESULTS: Openness was associated with verbal fluency and Agreeableness with immediate free recall. In contrast, no association between inflammatory markers and personality traits or cognition was identified. DISCUSSION: In elderly individuals without dementia, a high level of Openness or Agreeableness was associated with executive functioning/semantic memory and episodic memory, respectively

Poverty and inequality in real-world schizophrenia: a national study

BackgroundSchizophrenia has high socioeconomic impact among severe psychiatric disorders.AimsTo explore clinician-reported and patient-reported inequities between patients under the poverty threshold vs. the others.Method916 patients consecutively recruited in 10 national centers received a comprehensive standardized evaluation of illness severity, addictions and patient-reported outcomes.Results739 (80.7%) of the patients were classified in the poverty group. This group had poorer objective illness outcomes (lower positive, negative, cognitive, excitement/aggressive and self-neglect symptoms and lifetime history of planned suicide) in multivariate analyses. While they had similar access to treatments and psychotherapy, they had lower access to socially useful activities, couple’s life, housing and parenthood. They had also more disturbed metabolic parameters. On the contrary, the poverty group reported better self-esteem. No significant difference for depression, risky health behavior including addictions and sedentary behavior was found.InterpretationThe equity in access to care is attributed to the French social system. However, mental and physical health remain poorer in these patients, and they still experience poor access to social roles independently of illness severity and despite healthcare interventions. These patients may have paradoxically better self-esteem due to decreased contact with society and therefore lower stigma exposure (especially at work). Schizophrenia presents itself as a distinct impoverished population concerning health-related outcomes and social integration, warranting focus in public health initiatives and improved treatment, including tailored interventions, collaborative care models, accessible mental health services, housing support, vocational training and employment support, community integration, education and awareness, research and data collection, culturally competent approaches, and long-term support