Calibration and evaluation of individual-based models using Approximate Bayesian Computation

This paper investigates the feasibility of using approximate Bayesian computation (ABC) to calibrate and evaluate complex individual-based models (IBMs). As ABC evolves, various versions are emerging, but here we only explore the most accessible version, rejection-ABC. Rejection-ABC involves running models a large number of times, with parameters drawn randomly from their prior distributions, and then retaining the simulations closest to the observations. Although well-established in some fields, whether ABC will work with ecological IBMs is still uncertain. Rejection-ABC was applied to an existing 14-parameter earthworm energy budget IBM for which the available data consist of body mass growth and cocoon production in four experiments. ABC was able to narrow the posterior distributions of seven parameters, estimating credible intervals for each. ABC’s accepted values produced slightly better fits than literature values do. The accuracy of the analysis was assessed using cross-validation and coverage, currently the best available tests. Of the seven unnarrowed parameters, ABC revealed that three were correlated with other parameters, while the remaining four were found to be not estimable given the data available. It is often desirable to compare models to see whether all component modules are necessary. Here we used ABC model selection to compare the full model with a simplified version which removed the earthworm’s movement and much of the energy budget. We are able to show that inclusion of the energy budget is necessary for a good fit to the data. We show how our methodology can inform future modelling cycles, and briefly discuss how more advanced versions of ABC may be applicable to IBMs. We conclude that ABC has the potential to represent uncertainty in model structure, parameters and predictions, and to embed the often complex process of optimizing an IBM’s structure and parameters within an established statistical framework, thereby making the process more transparent and objective.

The neurogenic potential of astrocytes is regulated by inflammatory signals

Although the adult brain contains neural stem cells (NSCs) that generate new neurons throughout life, these astrocyte-like populations are restricted to two discrete niches. Despite their terminally differentiated phenotype, adult parenchymal astrocytes can re-acquire NSC-like characteristics following injury, and as such, these 'reactive' astrocytes offer an alternative source of cells for central nervous system (CNS) repair following injury or disease. At present, the mechanisms that regulate the potential of different types of astrocytes are poorly understood. We used in vitro and ex vivo astrocytes to identify candidate pathways important for regulation of astrocyte potential. Using in vitro neural progenitor cell (NPC)-derived astrocytes, we found that exposure of more lineage-restricted astrocytes to either tumor necrosis factor alpha (TNF-α) (via nuclear factor-κB (NFκB)) or the bone morphogenetic protein (BMP) inhibitor, noggin, led to re-acquisition of NPC properties accompanied by transcriptomic and epigenetic changes consistent with a more neurogenic, NPC-like state. Comparative analyses of microarray data from in vitro-derived and ex vivo postnatal parenchymal astrocytes identified several common pathways and upstream regulators associated with inflammation (including transforming growth factor (TGF)-β1 and peroxisome proliferator-activated receptor gamma (PPARγ)) and cell cycle control (including TP53) as candidate regulators of astrocyte phenotype and potential. We propose that inflammatory signalling may control the normal, progressive restriction in potential of differentiating astrocytes as well as under reactive conditions and represent future targets for therapies to harness the latent neurogenic capacity of parenchymal astrocytes.

Predicting how many animals will be where: how to build, calibrate and evaluate individual-based models

Individual-based models (IBMs) can simulate the actions of individual animals as they interact with one another and the landscape in which they live. When used in spatially-explicit landscapes IBMs can show how populations change over time in response to management actions. For instance, IBMs are being used to design strategies of conservation and of the exploitation of fisheries, and for assessing the effects on populations of major construction projects and of novel agricultural chemicals. In such real world contexts, it becomes especially important to build IBMs in a principled fashion, and to approach calibration and evaluation systematically. We argue that insights from physiological and behavioural ecology offer a recipe for building realistic models, and that Approximate Bayesian Computation (ABC) is a promising technique for the calibration and evaluation of IBMs. IBMs are constructed primarily from knowledge about individuals. In ecological applications the relevant knowledge is found in physiological and behavioural ecology, and we approach these from an evolutionary perspective by taking into account how physiological and behavioural processes contribute to life histories, and how those life histories evolve. Evolutionary life history theory shows that, other things being equal, organisms should grow to sexual maturity as fast as possible, and then reproduce as fast as possible, while minimising per capita death rate. Physiological and behavioural ecology are largely built on these principles together with the laws of conservation of matter and energy. To complete construction of an IBM information is also needed on the effects of competitors, conspecifics and food scarcity; the maximum rates of ingestion, growth and reproduction, and life-history parameters. Using this knowledge about physiological and behavioural processes provides a principled way to build IBMs, but model parameters vary between species and are often difficult to measure. A common solution is to manually compare model outputs with observations from real landscapes and so to obtain parameters which produce acceptable fits of model to data. However, this procedure can be convoluted and lead to over-calibrated and thus inflexible models. Many formal statistical techniques are unsuitable for use with IBMs, but we argue that ABC offers a potential way forward. It can be used to calibrate and compare complex stochastic models and to assess the uncertainty in their predictions. We describe methods used to implement ABC in an accessible way and illustrate them with examples and discussion of recent studies. Although much progress has been made, theoretical issues remain, and some of these are outlined and discussed.

Simulating the effects of mid- to upper-tropospheric clouds on microwave emissions in EC-Earth using COSP

In this work, the Cloud Feedback Model Intercomparison (CFMIP) Observation Simulation Package (COSP) is expanded to include scattering and emission effects of clouds and precipitation at passive microwave frequencies. This represents an advancement over the official version of COSP (version 1.4.0) in which only clear-sky brightness temperatures are simulated. To highlight the potential utility of this new microwave simulator, COSP results generated using the climate model EC-Earth's version 3 atmosphere as input are compared with Microwave Humidity Sounder (MHS) channel (190.311 GHz) observations. Specifically, simulated seasonal brightness temperatures (TB) are contrasted with MHS observations for the period December 2005 to November 2006 to identify possible biases in EC-Earth's cloud and atmosphere fields. The EC-Earth's atmosphere closely reproduces the microwave signature of many of the major large-scale and regional scale features of the atmosphere and surface. Moreover, greater than 60 % of the simulated TB are within 3 K of the NOAA-18 observations. However, COSP is unable to simulate sufficiently low TB in areas of frequent deep convection. Within the Tropics, the model's atmosphere can yield an underestimation of TB by nearly 30 K for cloudy areas in the ITCZ. Possible reasons for this discrepancy include both incorrect amount of cloud ice water in the model simulations and incorrect ice particle scattering assumptions used in the COSP microwave forward model. These multiple sources of error highlight the non-unique nature of the simulated satellite measurements, a problem exacerbated by the fact that EC-Earth lacks detailed micro-physical parameters necessary for accurate forward model calculations. Such issues limit the robustness of our evaluation and suggest a general note of caution when making COSP-satellite observation evaluations.

Systematic and random errors between collocated satellite ice water path observations

There remains large disagreement between ice-water path (IWP) in observational data sets, largely because the sensors observe different parts of the ice particle size distribution. A detailed comparison of retrieved IWP from satellite observations in the Tropics (!30 " latitude) in 2007 was made using collocated measurements. The radio detection and ranging(radar)/light detection and ranging (lidar) (DARDAR) IWP data set, based on combined radar/lidar measurements, is used as a reference because it provides arguably the best estimate of the total column IWP. For each data set, usable IWP dynamic ranges are inferred from this comparison. IWP retrievals based on solar reflectance measurements, in the moderate resolution imaging spectroradiometer (MODIS), advanced very high resolution radiometer–based Climate Monitoring Satellite Applications Facility (CMSAF), and Pathfinder Atmospheres-Extended (PATMOS-x) datasets, were found to be correlated with DARDAR over a large IWP range (~20–7000 g m -2 ). The random errors of the collocated data sets have a close to lognormal distribution, and the combined random error of MODIS and DARDAR is less than a factor of 2, which also sets the upper limit for MODIS alone. In the same way, the upper limit for the random error of all considered data sets is determined. Data sets based on passive microwave measurements, microwave surface and precipitation products system (MSPPS), microwave integrated retrieval system (MiRS), and collocated microwave only (CMO), are largely correlated with DARDAR for IWP values larger than approximately 700 g m -2 . The combined uncertainty between these data sets and DARDAR in this range is slightly less MODIS-DARDAR, but the systematic bias is nearly an order of magnitude.

Spectacular foodscapes: food celebrities and the politics of lifestyle mediation in an age of inequality

This editorial introduces a special issue of Food, Culture & Society and works to add a parallel, substantive take on the phenomenon of the food celebrity and the mediated, everyday cultural politics they create. We start by exploring the concept of the foodscape. Specifically, we argue that food celebrities represent a fundamental component of contemporary foodscapes, how they “perform” and function, and the socio-material means by which they are produced. We then explore the key roles and privileges of food celebrity, arguing that the celebrity chef is not the only high-profile, mediating figure at work on the foodscape. Key food celebrity paradoxes are identified and discussed: food celebrities must work to be authentic and aspirational, accessible yet exclusive, responsibilizing but also empowering. We conclude with a short contextualization of the papers in this special issue, and argue for the rich potential of food celebrity scholarship as a way to better understand food inequalities

Disparity-defined objects moving in depth do not elicit three-dimensional shape constancy

Observers generally fail to recover three-dimensional shape accurately from binocular disparity. Typically, depth is overestimated at near distances and underestimated at far distances [Johnston, E. B. (1991). Systematic distortions of shape from stereopsis. Vision Research, 31, 1351–1360]. A simple prediction from this is that disparity-defined objects should appear to expand in depth when moving towards the observer, and compress in depth when moving away. However, additional information is provided when an object moves from which 3D Euclidean shape can be recovered, be this through the addition of structure from motion information [Richards, W. (1985). Structure from stereo and motion. Journal of the Optical Society of America A, 2, 343–349], or the use of non-generic strategies [Todd, J. T., & Norman, J. F. (2003). The visual perception of 3-D shape from multiple cues: Are observers capable of perceiving metric structure? Perception and Psychophysics, 65, 31–47]. Here, we investigated shape constancy for objects moving in depth. We found that to be perceived as constant in shape, objects needed to contract in depth when moving toward the observer, and expand in depth when moving away, countering the effects of incorrect distance scaling (Johnston, 1991). This is a striking example of the failure of shape con- stancy, but one that is predicted if observers neither accurately estimate object distance in order to recover Euclidean shape, nor are able to base their responses on a simpler processing strategy.

Studies of aberrant phyllotaxy1 Mutants of Maize Indicate Complex Interactions between Auxin and Cytokinin Signaling in the Shoot Apical Meristem

One of the most fascinating aspects of plant morphology is the regular geometric arrangement of leaves and flowers, called phyllotaxy. The shoot apical meristem (SAM) determines these patterns, which vary depending on species and developmental stage. Auxin acts as an instructive signal in leaf initiation, and its transport has been implicated in phyllotaxy regulation in Arabidopsis (Arabidopsis thaliana). Altered phyllotactic patterns are observed in a maize (Zea mays) mutant, aberrant phyllotaxy1 (abph1, also known as abphyl1), and ABPH1 encodes a cytokinin-inducible type A response regulator, suggesting that cytokinin signals are also involved in the mechanism by which phyllotactic patterns are established. Therefore, we investigated the interaction between auxin and cytokinin signaling in phyllotaxy. Treatment of maize shoots with a polar auxin transport inhibitor, 1-naphthylphthalamic acid, strongly reduced ABPH1 expression, suggesting that auxin or its polar transport is required for ABPH1 expression. Immunolocalization of the PINFORMED1 (PIN1) polar auxin transporter revealed that PIN1 expression marks leaf primordia in maize, similarly to Arabidopsis. Interestingly, maize PIN1 expression at the incipient leaf primordium was greatly reduced in abph1 mutants. Consistently, auxin levels were reduced in abph1, and the maize PIN1 homolog was induced not only by auxin but also by cytokinin treatments. Our results indicate distinct roles for ABPH1 as a negative regulator of SAM size and a positive regulator of PIN1 expression. These studies highlight a complex interaction between auxin and cytokinin signaling in the specification of phyllotactic patterns and suggest an alternative model for the generation of altered phyllotactic patterns in abph1 mutants. We propose that reduced auxin levels and PIN1 expression in abph1 mutant SAMs delay leaf initiation, contributing to the enlarged SAM and altered phyllotaxy of these mutants.

Classroom at the New York Trade School

An empty classroom is shown here at the New York Trade School. This was likely a piano tuning classroom. Black and white photograph with some damage around the edges.

Piano Tuning Classroom

A Wissner piano is shown in a piano tuning classroom at the New York Trade School. Wissner pianos were manufactured in Brooklyn from 1878 until the company went out of business at the start of World War II. Black and white photograph.

Professor and Student in Piano Crafts Department

Here a professor in the Piano Crafts Department at the New York Trade School is shown helping a student. Black and white photograph.

Thick viewing : empirical examples of condensed moments of narrative impact in fiction film developing theoretical concepts for intensified engagements

Abstract  In a case study about viewing habits in a Swedish audience I sampled 309 questionnaires; interviews with five focus group were conducted together with ten in-depth individual interviews discussing altogether fifteen favorite films exploring specific scenes of idiosyncratic relevance.  The outcome supports claims about viewers as active and playful (cf. Höijer 1998, Frampton 2006, Hoover 2006, Plantinga 2009). In line with mediatization theory I also argue that spiritual meaning making takes place through mediated experiences and I support theories about fiction films as important sources for moral and spiritual reflection (Partridge 2004, Zillman 2005, Lynch 2007, Plantinga 2009). What Hjarvard calls the soft side of mediatization processes (2008) is illustrated showing adults experiencing enchantment through favorite films (Jerslev 2006, Partridge 2008, Klinger 2008, Oliver & Hartmann 2010).  Vernacular meaning making embedded in everyday life and spectators dealing with fiction narratives such as Gladiator, Amelie from Montmartre or Avatar highlights the need for a more nuanced understanding of elevated cinematic experiences. The reported impact of specific movies is analyzed through theories where cognition and affect are central aspects of spectators’ engagements with a film (Tan 1996, Caroll 1999, Grodal 2009). Crucially important are theories of meaning-making where viewers’ detailed interpretation of specific scenes are embedded in high-level meaning-making where world view issues and spectators’ moral frameworks are activated (Zillman 2005, Andersson & Andersson 2005, Frampton 2006, Lynch 2007, Avila 2007, Axelson 2008, Plantinga 2009).  Also results from a growing body of empirical oriented research in film studies are relevant with an interest in what happens with the flesh and blood spectator exposed to filmic narratives (Jerslev 2006, Klinger 2008, Barker 2009, Suckfüll 2010, Oliver & Hartmann 2010). Analyzing the qualitative results of my case study, I want to challenge the claim that the viewer has to suspend higher order reflective cognitive structures in order to experience suture (Butler & Palesh 2004). What I find in my empirical examples is responses related to spectators’ highest levels of mental activity, all anchored in the sensual-emotional apparatus (Grodal 2009). My outcome is in line with a growing number of empirical case studies which support conclusions that both thinking and behavior are affected by film watching (Marsh 2007, Sückfull 2010, Oliver & Hartmann 2010, Axelson forthcoming). The presentation contributes to a development of concepts which combines aesthetic, affective and cognitive components in an investigation of spectator’s moves from emotional evaluation of intra-text narration to extra-textual assessments, testing the narrative for larger significance in idiosyncratic ways (Bordwell & Thompson 1997, Marsh 2007, Johnston 2007, Bruun Vaage 2009, Axelson 2011). There are a several profitable concepts suggested to embrace the complex interplay between affects, cognition and emotions when individuals respond to fictional narratives. Robert K. Johnston label it “deepening gaze” (2007: 307) and “transformative viewing” (2007: 305). Philosopher Mitch Avila proposes “high cognition” (2007: 228) and Casper Thybjerg ”higher meaning” (2008: 60). Torben Grodal talks about “feelings of deep meaning” (Grodal 2009: 149). With a nod to Clifford Geertz, Craig Detweiler adopts “thick description” (2007: 47) as do Kutter Callaway altering it to ”thick interpretations” (Callaway 2013: 203).  Frampton states it in a paradox; ”affective intelligence” (Frampton 2006: 166). As a result of the empirical investigation, inspired by Geertz, Detweiler & Callaway, I advocate thick viewing for capturing the viewing process of these specific moments of film experience when profound and intensified emotional interpretations take place. The author As a sociologist of religion, Tomas Axelsons research deals with people’s use of mediated narratives to make sense of reality in a society characterized by individualization, mediatization and pluralized world views.  He explores uses of fiction film as a resource in every day life and he is currently finishing his three year project funded by the Swedish Research Council: Spectator engagement in film and utopian self-reflexivity. Moving Images and Moved Minds. http://www.du.se/sv/AVM/Personal/Tomas-Axelson Bibliography Axelson, T. (Forthcoming 2014). Den rörliga bildens förmåga att beröra.[1] Stockholm: Liber Axelson, T. (In peer review). Vernacular Meaning Making. Examples of narrative impact in fiction film questioning the ’banal’ notion in mediatization theory. Nordicom Review. Nordicom Göteborg. Axelson, T. (2011). Människans behov av fiktion. Den rörliga bildens förmåga att beröra människan på djupet.[2]Kulturella perspektiv. Volume 2. Article retrieved from www.kultmed.umu.se/digitalAssets/74/74304_axelson-22011.pdf Axelson, Tomas (2010) “Narration, Visualization and Mind. Movies in everyday life as a resource for utopian self-reflection.” Paper presentation at CMRC, 7th Conference of Media, Religion & Culture in Toronto, Canada 9 – 13th August 2010. Axelson, Tomas (2008) Movies and Meaning. Studying Audience, Favourite Films and Existential Matters. Particip@tions : Journal of Audience and Reception Studies. Volume 5, (1). Doctoral dissertation summary. ACTA UNIVERSITATIS UPSALIENSIS. Article retrieved from http://www.participations.org/Volume%205/Issue%201%20-%20special/5_01_axelson.htm  [1] English translation: Moving Images and Moved Minds. [2] English translation: Our need for fiction. Deeply Moved by Moving Images. Cultural Perspectives.

Estudo de obtenção de número estrutural em pavimentos flexíveis

O presente trabalho estuda a obtenção de número estrutural em pavimentos flexíveis existentes. O estudo foi realizado em trechos pertencentes a duas regiões do Rio Grande do Sul, com a mesma formação geológica. De posse dos dados de levantamentos das deflexões obtidos com um equipamento tipo FWD (Falling Weight Deflectometer) e, com valores das espessuras dos pavimentos fornecidas pelo DAER-RS, foram realizadas retroanálises de todas as bacias de deformação levantadas, para cada ponto dos trechos estudados. Encontrados os Módulos de Resiliência de cada camada dos pavimentos, foram determinados, através das correlações da AASHTO (American Association of State Highway and Transportation Officials), os coeficientes estruturais e conseqüentemente os números estruturais para cada camada de pavimento. Por outro lado, determinou-se o raio de curvatura, para cada ponto levantado pelo equipamento, através da parábola de segundo grau utilizada pelo DNER (Departamento Nacional de Estradas de Rodagens). Verificou-se que os valores de número estrutural dos pavimentos e os raios de curvatura variam em proporções semelhantes, permitindo então a identificação de correlações entre os mesmos. As correlações entre raio de curvatura e número estrutural apresentadas neste trabalho facilitam a obtenção do número estrutural, sem utilizar retroanálises.