Representation errors and retrievals in linear and nonlinear data assimilation

This article shows how one can formulate the representation problem starting from Bayes’ theorem. The purpose of this article is to raise awareness of the formal solutions,so that approximations can be placed in a proper context. The representation errors appear in the likelihood, and the different possibilities for the representation of reality in model and observations are discussed, including nonlinear representation probability density functions. Specifically, the assumptions needed in the usual procedure to add a representation error covariance to the error covariance of the observations are discussed,and it is shown that, when several sub-grid observations are present, their mean still has a representation error ; socalled ‘superobbing’ does not resolve the issue. Connection is made to the off-line or on-line retrieval problem, providing a new simple proof of the equivalence of assimilating linear retrievals and original observations. Furthermore, it is shown how nonlinear retrievals can be assimilated without loss of information. Finally we discuss how errors in the observation operator model can be treated consistently in the Bayesian framework, connecting to previous work in this area.

A land cover map of Latin America and the Caribbean in the framework of the SERENA project

Land cover maps at different resolutions and mapping extents contribute to modeling and support decision making processes. Because land cover affects and is affected by climate change, it is listed among the 13 terrestrial essential climate variables. This paper describes the generation of a land cover map for Latin America and the Caribbean (LAC) for the year 2008. It was developed in the framework of the project Latin American Network for Monitoring and Studying of Natural Resources (SERENA), which has been developed within the GOFC-GOLD Latin American network of remote sensing and forest fires (RedLaTIF). The SERENA land cover map for LAC integrates: 1) the local expertise of SERENA network members to generate the training and validation data, 2) a methodology for land cover mapping based on decision trees using MODIS time series, and 3) class membership estimates to account for pixel heterogeneity issues. The discrete SERENA land cover product, derived from class memberships, yields an overall accuracy of 84% and includes an additional layer representing the estimated per-pixel confidence. The study demonstrates in detail the use of class memberships to better estimate the area of scarce classes with a scattered spatial distribution. The land cover map is already available as a printed wall map and will be released in digital format in the near future. The SERENA land cover map was produced with a legend and classification strategy similar to that used by the North American Land Change Monitoring System (NALCMS) to generate a land cover map of the North American continent, that will allow to combine both maps to generate consistent data across America facilitating continental monitoring and modeling

Generation and analysis of the 2005 land cover map for Mexico using 250m MODIS data

Land cover plays a key role in global to regional monitoring and modeling because it affects and is being affected by climate change and thus became one of the essential variables for climate change studies. National and international organizations require timely and accurate land cover information for reporting and management actions. The North American Land Change Monitoring System (NALCMS) is an international cooperation of organizations and entities of Canada, the United States, and Mexico to map land cover change of North America's changing environment. This paper presents the methodology to derive the land cover map of Mexico for the year 2005 which was integrated in the NALCMS continental map. Based on a time series of 250 m Moderate Resolution Imaging Spectroradiometer (MODIS) data and an extensive sample data base the complexity of the Mexican landscape required a specific approach to reflect land cover heterogeneity. To estimate the proportion of each land cover class for every pixel several decision tree classifications were combined to obtain class membership maps which were finally converted to a discrete map accompanied by a confidence estimate. The map yielded an overall accuracy of 82.5% (Kappa of 0.79) for pixels with at least 50% map confidence (71.3% of the data). An additional assessment with 780 randomly stratified samples and primary and alternative calls in the reference data to account for ambiguity indicated 83.4% overall accuracy (Kappa of 0.80). A high agreement of 83.6% for all pixels and 92.6% for pixels with a map confidence of more than 50% was found for the comparison between the land cover maps of 2005 and 2006. Further wall-to-wall comparisons to related land cover maps resulted in 56.6% agreement with the MODIS land cover product and a congruence of 49.5 with Globcover.

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely-related crop species, lentil, and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2 cM interval of Vf chromosome 2 which was highly collinear with Mt3. The obvious candidate gene from 77 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene (Mt3g092830, Mt3g092840) controlling anthocyanin production in Medicago and re-sequencing of the Vf orthologue showed a putative causative deletion of the entire 5’ end of the gene.

Instantaneous threat detection based on a semantic representation of activities, zones and trajectories

Threat detection is a challenging problem, because threats appear in many variations and differences to normal behaviour can be very subtle. In this paper, we consider threats on a parking lot, where theft of a truck’s cargo occurs. The threats range from explicit, e.g. a person attacking the truck driver, to implicit, e.g. somebody loitering and then fiddling with the exterior of the truck in order to open it. Our goal is a system that is able to recognize a threat instantaneously as they develop. Typical observables of the threats are a person’s activity, presence in a particular zone and the trajectory. The novelty of this paper is an encoding of these threat observables in a semantic, intermediate-level representation, based on low-level visual features that have no intrinsic semantic meaning themselves. The aim of this representation was to bridge the semantic gap between the low-level tracks and motion and the higher-level notion of threats. In our experiments, we demonstrate that our semantic representation is more descriptive for threat detection than directly using low-level features. We find that a person’s activities are the most important elements of this semantic representation, followed by the person’s trajectory. The proposed threat detection system is very accurate: 96.6 % of the tracks are correctly interpreted, when considering the temporal context.

The representation of the West-African Monsoon vertical cloud structure in the Met Office Unified Model: an evaluation with CloudSat

Weather and climate model simulations of the West African Monsoon (WAM) have generally poor representation of the rainfall distribution and monsoon circulation because key processes, such as clouds and convection, are poorly characterized. The vertical distribution of cloud and precipitation during the WAM are evaluated in Met Office Unified Model simulations against CloudSat observations. Simulations were run at 40-km and 12-km horizontal grid length using a convection parameterization scheme and at 12-km, 4-km, and 1.5-km grid length with the convection scheme effectively switched off, to study the impact of model resolution and convection parameterization scheme on the organisation of tropical convection. Radar reflectivity is forward-modelled from the model cloud fields using the CloudSat simulator to present a like-with-like comparison with the CloudSat radar observations. The representation of cloud and precipitation at 12-km horizontal grid length improves dramatically when the convection parameterization is switched off, primarily because of a reduction in daytime (moist) convection. Further improvement is obtained when reducing model grid length to 4 km or 1.5 km, especially in the representation of thin anvil and mid-level cloud, but three issues remain in all model configurations. Firstly, all simulations underestimate the fraction of anvils with cloud top height above 12 km, which can be attributed to too low ice water contents in the model compared to satellite retrievals. Secondly, the model consistently detrains mid-level cloud too close to the freezing level, compared to higher altitudes in CloudSat observations. Finally, there is too much low-level cloud cover in all simulations and this bias was not improved when adjusting the rainfall parameters in the microphysics scheme. To improve model simulations of the WAM, more detailed and in-situ observations of the dynamics and microphysics targeting these non-precipitating cloud types are required.

Improved seasonal prediction of the hot summer of 2003 over Europe through better representation of uncertainty in the land surface

Methods to explicitly represent uncertainties in weather and climate models have been developed and refined over the past decade, and have reduced biases and improved forecast skill when implemented in the atmospheric component of models. These methods have not yet been applied to the land surface component of models. Since the land surface is strongly coupled to the atmospheric state at certain times and in certain places (such as the European summer of 2003), improvements in the representation of land surface uncertainty may potentially lead to improvements in atmospheric forecasts for such events. Here we analyse seasonal retrospective forecasts for 1981–2012 performed with the European Centre for Medium-Range Weather Forecasts’ (ECMWF) coupled ensemble forecast model. We consider two methods of incorporating uncertainty into the land surface model (H-TESSEL): stochastic perturbation of tendencies, and static perturbation of key soil parameters. We find that the perturbed parameter approach considerably improves the forecast of extreme air temperature for summer 2003, through better representation of negative soil moisture anomalies and upward sensible heat flux. Averaged across all the reforecasts the perturbed parameter experiment shows relatively little impact on the mean bias, suggesting perturbations of at least this magnitude can be applied to the land surface without any degradation of model climate. There is also little impact on skill averaged across all reforecasts and some evidence of overdispersion for soil moisture. The stochastic tendency experiments show a large overdispersion for the soil temperature fields, indicating that the perturbation here is too strong. There is also some indication that the forecast of the 2003 warm event is improved for the stochastic experiments, however the improvement is not as large as observed for the perturbed parameter experiment.

Breaching the social contract: crises of democratic representation and patterns of extreme right party support

Why has the extreme right Greek Golden Dawn, a party with clear links to fascism experienced a rise defying all theories that claim that such a party is unlikely to win in post-WWII Europe? And, if we accept that economic crisis is an explanation for this, why has such a phenomenon not occurred in other countries that have similar conducive conditions, such as Portugal and Spain? This article addresses this puzzle by (a) carrying out a controlled comparison of Greece, Portugal and Spain and (b) showing that the rise of the extreme right is not a question of intensity of economic crisis. Rather it is the nature of the crisis, i.e. economic versus overall crisis of democratic representation that facilitates the rise of the extreme right. We argue that extreme right parties are more likely to experience an increase in their support when economic crisis culminates into an overall crisis of democratic representation. Economic crisis is likely to become a political crisis when severe issues of governability impact upon the ability of the state to fulfil its social contract obligations. This breach of the social contract is accompanied by declining levels of trust in state institutions, resulting in party system collapse.

Communicating thematic data quality with web map services

Geospatial information of many kinds, from topographic maps to scientific data, is increasingly being made available through web mapping services. These allow georeferenced map images to be served from data stores and displayed in websites and geographic information systems, where they can be integrated with other geographic information. The Open Geospatial Consortium’s Web Map Service (WMS) standard has been widely adopted in diverse communities for sharing data in this way. However, current services typically provide little or no information about the quality or accuracy of the data they serve. In this paper we will describe the design and implementation of a new “quality-enabled” profile of WMS, which we call “WMS-Q”. This describes how information about data quality can be transmitted to the user through WMS. Such information can exist at many levels, from entire datasets to individual measurements, and includes the many different ways in which data uncertainty can be expressed. We also describe proposed extensions to the Symbology Encoding specification, which include provision for visualizing uncertainty in raster data in a number of different ways, including contours, shading and bivariate colour maps. We shall also describe new open-source implementations of the new specifications, which include both clients and servers.

Low rank representation on Riemannian manifold of symmetric positive definite matrices

Sparse coding aims to find a more compact representation based on a set of dictionary atoms. A well-known technique looking at 2D sparsity is the low rank representation (LRR). However, in many computer vision applications, data often originate from a manifold, which is equipped with some Riemannian geometry. In this case, the existing LRR becomes inappropriate for modeling and incorporating the intrinsic geometry of the manifold that is potentially important and critical to applications. In this paper, we generalize the LRR over the Euclidean space to the LRR model over a specific Rimannian manifold—the manifold of symmetric positive matrices (SPD). Experiments on several computer vision datasets showcase its noise robustness and superior performance on classification and segmentation compared with state-of-the-art approaches.

Reply to: punishing food: what brain activity can tell us about the representation of food in recovered anorexia nervosa

Eating disorders are characterized by aberrant cognitions and behaviors around food. We used a novel functional magnetic resonance imaging task in a sample of recovered anorexia nervosa subjects to study the neural response to both pleasant and aversive food tastes and pictures compared with a group of matched female subjects who had never had the disorder. We report that individuals recovered from anorexia nervosa have an increased neural response to rewarding and aversive food stimuli, in the form of chocolate (e.g., in the ventral striatum) and moldy strawberries (e.g., in the caudate).

Regulation of the ERK subgroup of MAP kinase cascades through G protein-coupled receptors.

The extracellularly-responsive kinase (ERK) subfamily of mitogen-activated protein kinases (MAPKs) has been implicated in the regulation of cell growth and differentiation. Activation of ERKs involves a two-step protein kinase cascade lying upstream from ERK, in which the Raf family are the MAPK kinase kinases and the MEK1/MEK2 isoforms are the MAPK kinases. The linear sequence of Raf --> MEK --> ERK constitutes the ERK cascade. Although the ERK cascade is activated through growth factor-regulated receptor protein tyrosine kinases, they are also modulated through G protein-coupled receptors (GPCRs). All four G protein subfamilies (Gq/11 Gi/o, Gs and G12/13) influence the activation state of ERKs. In this review, we describe the ERK cascade and characteristics of its activation through GPCRs. We also discuss the identity of the intervening steps that may couple agonist binding at GPCRs to activation of the ERK cascade.