Game-based tools to transmit freshwater ecology concepts

International audienceThere is an increasing expectation on people to be aware and to get involved in the environmental issues that our world is facing. However, expert knowledge is often required to understand most of these issues. One of the challenges in science today lies in explaining complex issues in a simple and understandable way to an unspecialized audience. Games can turn out to be a good medium for scientific vulgarization. Indeed, the first form of learning we all experienced was by playing. Games are very popular, and from an educational point of view, they present many advantages. They are dynamic and interactive. Therefore, the player engagement increases, as well as its knowledge retention. In addition, the player is immersed into a new world and discovers a virtual environment where he needs to develop strategies and to identify crucial processes. Those characteristics can be wisely used to spread scientific topics, and gamification has already been proposed as a tool for an easier propagation of scientific thinking such as in pharmacology or geosciences. In this context, our project aims at developing game-based tools to transmit the basic concepts of freshwater ecology. We choose to focus on a classical board game and on a computer based game because they are complementary in the targeted audience (groups versus online gamers) and the possibilities offered, in particular regarding the interactions between players and the system dynamics. The general methodology is divided in five steps: (1) selection of species; (2) definition of the instructions (object, game board, rules); (3) incorporation of environmental stressors (biotic and abiotic), (4) design and construction of interfaces (board and computer model); (5) test with players. All steps are necessarily interdependent and are tackled in parallel during the development of the games. While the board game is inspired by past experiences of player, the computer game is based on a model of simulation of the ecosystem. In order to introduce notions of equilibrium and its perturbations that occur at a larger time scale than on the board game, we propose to implement an agent-based model (ABM) and to couple its dynamics with gaming actions. ABM have already been widely used in ecology. Therefore, we selected a trophic chain dynamic model (extended prey-predator model) that can capture fish behavioral rules and spatially heterogeneous environment. It is particularly suitable for the game implementation: fish behaviors are influenced by players whereas the ecosystem is disturbed by external events. Both games are based on the same general rules, even if slight modifications have to be expected according to the type of game. Table 1 gives an overview on how the game can be introduced to a specific audience: The virtual ecosystem is presented from a fish perspective. The object of the game is to reach a given number of adults and juveniles that will guarantee the stability of the population in the lake. For this purpose, each player has to find resources accordingly to his fish species. The resources are converted into “units” that can be used thereafter by the player for different purposes, such as reproduction, juvenile growth, to escape a predator or to attack a pray. The external perturbations are illustrated by “events” that are supposed to reflect abiotic (e.g. water temperature, light, water scarcity) and biotic (e.g. chemicals, parasites, fisherman) stressors. The current version of the game includes four players, each of them being a different species, namely the roach (Rutilus rutilus), the pumpkinseed (Lepomis gibbosus), the zander (Sander lucioperca), and the bleak (Alburnus alburnus). The rationale behind lies in maximizing interactions between players (predation and competition, see fig. 1) and to illustrate feeding and reproduction strategies from different perspectives (from a big solitary fish to a shoal fish, including a invasive fish species). The board is basically composed of boxes. Each of them represents a type of resource (e.g. crustacean, plants, insects), and some boxes are combined with an “event” to include the external perturbations in the game. The player has 2 token on the board (one male and one female) and is moving them by throwing dice. The ecological characteristics of each species are kept on a record paper by each player. It describes the species-specific rules (feeding preferences, time and resources needed to reproduce, how to escape/attack etc). A first prototype is currently being tested to determine and adjust the board game design, the ecological characteristics of each species and the characterization of events, in particular their impacts on players. The design of the board is under progress and will figure the edge of a lake. The aforementioned species and natural ressources are the basis of the system. Discrete dynamics consist in the following steps : (a) wandering of species in their preferred zone of the lake; (b) trophic interactions (fish-fish and fish-ressources) ; (c) renewing of fish (reproduction) and of ressources. The model parameters include reproduction rates, movement parameters, etc. Large-scale model exploration and calibration are currently running in order to find parameter ranges at which ecosystem is in equilibrium1. The equilibrium will constitute the default state of the system without user control. User interactions are then integrated after each turn, at given time intervals (one month, when one time step is 6h for example). It allows the system to evolve in-between. During this time frame, the players observe the consequences of its actions and the reaction of the ecosystem to external events. Further developments will consist in model refinement and user latitude adjustments thanks to player feedbacks.A prototype of each game is currently available for testing and refinements are expected while experiencing the games. In a short term, next versions of the games will be developed after player feedback and will include the aesthetic design of the games and refined processes parameters. Mid-term and long-term objectives are oriented towards an online version of the computer game as described before, and the use of crowdfunding platforms to offer and diffuse the board game. The very first objective of our games remains to be entertaining, keeping in mind that the ludic rather than pedagogical aspects are central in the success of such game-based media. If players forget that the game is about ecology, our precise objective is reached. It would mean that the underlying scientific concepts are clearly understood

La médiathèque de la Cité de la musique

Ouverte le 27 octobre dernier, la nouvelle médiathèque forme une sorte de « pont » au coeur de la Cité, entre l’espace dédié au musée et celui des concerts. Visite guidée par sa directrice

O direito penal do inimigo: reconfiguração do Estado de Direito?

Hodiernamente temos vindo a assistir a um sentimento global de vulnerabilidade face a uma crescente desterritorialização do crime e da segurança1. Os efeitos do terrorismo e da criminalidade organizada já não se fazem sentir exclusivamente nos locais-alvo das acções terroristas, mas sim a uma escala mundial. Perante este clima de insegurança, aliado à actual crise de paradigma do Direito Penal, ergueram-se vozes em defesa de um novo modelo configurativo deste ramo do Direito, de forma a combater os novos perigos da sociedade a que caracterizaram de risco. Günther Jakobs assume o papel de voz predominante na construção deste movimento securitário o Direito Penal do inimigo, cujas características pretendemos analisar.Desta forma, esta Tese terá como propósito o estudo, ainda que de forma breve, do modelo de Direito Penal construído por Günther Jakobs Feindstrafrecht, em português: o Direito penal do inimigo e a sua relação com os princípios estruturantes do Estado de Direito, em especial, o princípio da dignidade da pessoa humana.No primeiro ponto principiaremos por abordar o novo modelo de Direito Penal proposto por Jakobs, enunciando as características que o distinguem do paradigma actual e que suscitaram uma dura reacção por parte da generalidade da doutrina. Faremos especial referência ao conceito de Terrorismo, onde será colocado em evidência o problema da harmonização dos valores da Paz e da Segurança com os Direitos, Liberdades e Garantias previstos na Constituição da República Portuguesa, que fazem parte do elenco basilar de princípios nos quais se funda o Estado de Direito. Terminaremos o capítulo em questão com uma breve referência aos efeitos produzidos pela teoria de Jakobs no actual paradigma do Direito Penal internacional, fazendo referência aos casos de Espanha, Reino Unido e Estados Unidos da América, quer pelo recente historial de actividade terrorista no seu território, quer pela natureza e amplitude das medidas políticas e legislativas adoptadas.No segundo capítulo será feita uma reflexão em torno de novas formas de restrição de direitos fundamentais com especial enfoque para os métodos de identificação e segurança que englobam o recurso a dados biométricos e a scanners corporais que surgiram no seguimento da expansão de um movimento que elegeu como estandarte o valor da Segurança, olvidando a importância da preservação de direitos fundamentais como o direito à reserva da intimidade da vida privada. São, pois, os novos ideais punitivos, cujos efeitos se têm feito sentir no Direito Penal �\xA0 escala mundial, que, aliados a uma crescente demanda de segurança, têm fomentado restrições ilícitas aos direitos, liberdades e garantias dos cidadãos.Por fim, ensaiaremos uma construção crítica à teoria de Jakobs, nomeadamente no que toca à sua harmonização com o princípio da dignidade da pessoa humana, aos limites que esta lhe impõe, o que implicará, consequentemente, uma análise da sua coadunação com o Estado de Direito

SoFiA: a flexible source finder for 3D spectral line data

We introduce SoFiA, a flexible software application for the detection and parameterization of sources in 3D spectral-line datasets. SoFiA combines for the first time in a single piece of software a set of new source-finding and parameterization algorithms developed on the way to future HI surveys with ASKAP (WALLABY, DINGO) and APERTIF. It is designed to enable the general use of these new algorithms by the community on a broad range of datasets. The key advantages of SoFiA are the ability to: search for line emission on multiple scales to detect 3D sources in a complete and reliable way, taking into account noise level variations and the presence of artefacts in a data cube; estimate the reliability of individual detections; look for signal in arbitrarily large data cubes using a catalogue of 3D coordinates as a prior; provide a wide range of source parameters and output products which facilitate further analysis by the user. We highlight the modularity of SoFiA, which makes it a flexible package allowing users to select and apply only the algorithms useful for their data and science questions. This modularity makes it also possible to easily expand SoFiA in order to include additional methods as they become available. The full SoFiA distribution, including a dedicated graphical user interface, is publicly available for download.Comment: MNRAS, accepted. SoFiA is registered at the Astrophysics Source Code Library with ID ascl:1412.001. Download SoFiA at https://github.com/SoFiA-Admin/SoFi

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

Mixture effects in samples of multiple contaminants – An inter-laboratory study with manifold bioassays

© 2018 Chemicals in the environment occur in mixtures rather than as individual entities. Environmental quality monitoring thus faces the challenge to comprehensively assess a multitude of contaminants and potential adverse effects. Effect-based methods have been suggested as complements to chemical analytical characterisation of complex pollution patterns. The regularly observed discrepancy between chemical and biological assessments of adverse effects due to contaminants in the field may be either due to unidentified contaminants or result from interactions of compounds in mixtures. Here, we present an interlaboratory study where individual compounds and their mixtures were investigated by extensive concentration-effect analysis using 19 different bioassays. The assay panel consisted of 5 whole organism assays measuring apical effects and 14 cell- and organism-based bioassays with more specific effect observations. Twelve organic water pollutants of diverse structure and unique known modes of action were studied individually and as mixtures mirroring exposure scenarios in freshwaters. We compared the observed mixture effects against component-based mixture effect predictions derived from additivity expectations (assumption of non-interaction). Most of the assays detected the mixture response of the active components as predicted even against a background of other inactive contaminants. When none of the mixture components showed any activity by themselves then the mixture also was without effects. The mixture effects observed using apical endpoints fell in the middle of a prediction window defined by the additivity predictions for concentration addition and independent action, reflecting well the diversity of the anticipated modes of action. In one case, an unexpectedly reduced solubility of one of the mixture components led to mixture responses that fell short of the predictions of both additivity mixture models. The majority of the specific cell- and organism-based endpoints produced mixture responses in agreement with the additivity expectation of concentration addition. Exceptionally, expected (additive) mixture response did not occur due to masking effects such as general toxicity from other compounds. Generally, deviations from an additivity expectation could be explained due to experimental factors, specific limitations of the effect endpoint or masking side effects such as cytotoxicity in in vitro assays. The majority of bioassays were able to quantitatively detect the predicted non-interactive, additive combined effect of the specifically bioactive compounds against a background of complex mixture of other chemicals in the sample. This supports the use of a combination of chemical and bioanalytical monitoring tools for the identification of chemicals that drive a specific mixture effect. Furthermore, we demonstrated that a panel of bioassays can provide a diverse profile of effect responses to a complex contaminated sample. This could be extended towards representing mixture adverse outcome pathways. Our findings support the ongoing development of bioanalytical tools for (i) compiling comprehensive effect-based batteries for water quality assessment, (ii) designing tailored surveillance methods to safeguard specific water uses, and (iii) devising strategies for effect-based diagnosis of complex contamination