Spatial statistical analysis and selection of genotypes in plant breeding

The objective of this study was to evaluate the efficiency of spatial statistical analysis in the selection of genotypes in a plant breeding program and, particularly, to demonstrate the benefits of the approach when experimental observations are not spatially independent. The basic material of this study was a yield trial of soybean lines, with five check varieties (of fixed effect) and 110 test lines (of random effects), in an augmented block design. The spatial analysis used a random field linear model (RFML), with a covariance function estimated from the residuals of the analysis considering independent errors. Results showed a residual autocorrelation of significant magnitude and extension (range), which allowed a better discrimination among genotypes (increase of the power of statistical tests, reduction in the standard errors of estimates and predictors, and a greater amplitude of predictor values) when the spatial analysis was applied. Furthermore, the spatial analysis led to a different ranking of the genetic materials, in comparison with the non-spatial analysis, and a selection less influenced by local variation effects was obtained.

Machine learning for spatial environmental data. Theory, applications and software

The book presents the state of the art in machine learning algorithms (artificial neural networks of different architectures, support vector machines, etc.) as applied to the classification and mapping of spatially distributed environmental data. Basic geostatistical algorithms are presented as well. New trends in machine learning and their application to spatial data are given, and real case studies based on environmental and pollution data are carried out. The book provides a CD-ROM with the Machine Learning Office software, including sample sets of data, that will allow both students and researchers to put the concepts rapidly to practice.

Spatial learning by rats across visually disconnected environments

Two spatial tasks were designed to test specific properties of spatial representation in rats. In the first task, rats were trained to locate an escape hole at a fixed position in a visually homogeneous arena. This arena was connected with a periphery where a full view of the room environment existed. Therefore, rats were dependent on their memory trace of the previous position in the periphery to discriminate a position within the central region. Under these experimental conditions, the test animals showed a significant discrimination of the training position without a specific local view. In the second task, rats were trained in a radial maze consisting of tunnels that were transparent at their distal ends only. Because the central part of the maze was non-transparent, rats had to plan and execute appropriate trajectories without specific visual feedback from the environment. This situation was intended to encourage the reliance on prospective memory of the non-visited arms in selecting the following move. Our results show that acquisition performance was only slightly decreased compared to that shown in a completely transparent maze and considerably higher than in a translucent maze or in darkness. These two series of experiments indicate (1) that rats can learn about the relative position of different places with no common visual panorama, and (2) that they are able to plan and execute a sequence of visits to several places without direct visual feed-back about their relative position.

L'équité d'accès aux ressources en eau : fin ou moyen d'amélioration de l'efficacité de l'irrigation ? : la gestion des ressources en eau dans l'état du Gujarat (Inde) dans la perpective de la political ecology

La thèse présentée ici est le résultat d'une étroite collaboration avec une ONG indienne, AKRSP(I), intervenant dans le développement de l'irrigation au Gujarat depuis plus de 25 ans. Un SIG prototype a été mis en oeuvre et nous permet de proposer ime analyse spatiale et quantitative de l'action de cette ONG ainsi qu'une réflexion plus générale sur les leviers de mise en valeur et de gestion des ressources en eau à des fins agricoles. On peut souligner trois principaux enseignements: Les perspectives d'application des SIG au sein des ONG sont manifestes. Les exigences des bailleurs de fonds peuvent néanmoins faire obstacle à leur développement car, indi-rectement, ils favorisent la mise en oeuvre de SI voués à la justification plutôt qu'à la planification et au suivi des programmes d'actions. Ce résultat soulève la question de la pertinence de l'encadrement, des critères d'évaluation et de la conditionnalité de l'aide publique au développement. Les ONG ont un fort potentiel pour participer à la mise en valeur des ressources en eau en Inde et aider à relever le défi agro-démographique indien, en particulier dans les zones marginales où les services étatiques sont en retrait. Les stratégies d'action basées principalement sur l'application des instruments économiques et techniques doivent cependant être modifiées. Nous montrons qu'elles favorisent une inégalité d'accès aux ressources qui débouche sur une efficacité limitée des pratiques d'irrigation, sur un plan agro-technique. Ces résultats soulignent la nécessité de poursuivre une réflexion critique des discours et solutions dominants en matière de gestion des ressources en eau. Deux pistes d'amélioration sont avancées: 1. considérer l'équité d'accès comme un moyen d'optimiser la gestion de la ressource (limiter le volume d'eau par agriculteur pour encourager les choix de cultures irriguées peu consommatrices et l'adoption des technologies d'économie d'eau), 2. prêter attention à l'ordre dans lequel les différents instruments de gestion disponibles sont employés afin de les articuler dans un séquençage temporel pertinent. La Political Ecology apparait comme un cadre conceptuel très pertinent pour engager cette réflexion critique. Elle permet d'intégrer différentes échelles d'asymétries de pouvoirs à la compréhension des situations et des blocages observables localement : inégalités de capabilités et forces socio-politiques à l'échelle locale, politiques agro-industrielles (coton) et jeux d'alliances politiques des castes à l'échelle nationale, discours et conflits idéologiques ou orientations stratégiques des bailleurs de fonds à l'échelle internationale... Notre recherche empirique contribue modestement au développement de cette Political Ecology de la mise en valeur et de la gestion des ressources en eau. - The present research is based on a close collaboration with an indian NGO, AKRSP(I), which is active in the development of irrigation facilities in Gujarat for the past 25 years. We built a GIS prototype providing quantitative and spatial datas to analyse the NGO intervention and propose a general reflection about water resources development and management issues. Three main findings may be emphasized : The potential of GIS within the workings of an NGO is obvious, as an information ma-nagement tool as much as for developing analytical capacity. However, financial backers expectations may not favour a relevant development of this technology. Indirectly, they promote Information Systems built to justify rather than to plan or monitor action pro¬grammes. This raises the question of stricter framework, conditionality criters and stan¬dardised assessment indicators surrounding official development assistance. There is strong potential that NGOs can assist with the improvement of water resources in India. They can help in overcoming Indian demographic-related agricultural challenges, especially in marginal rural areas neglected by state services. However, intervention strategies mainly based on technical and economic management tools has to be adapted. We found that they lead to inequitable access and distribution of water resources what induces a low efficiency of irrigation practices from an agro-technical point of view. These results underline the need to go further in criticizing dominant ideas and guidelines regarding water resources management. We suggest two other options : 1. to consider equitable access has a tool to improve the effective use of water for agricul¬tural purposes (limiting the volume of water available per farmer would encourage them to adopt low water consumption crops and water saving technics), 2. to consider more carefully the order of use of the various management tools available and to structure them in a relevant sequence. Here, Political Ecology seems to be a relevant conceptual framework to enter into such a critical reflection, integrating different levels and scales of political asymmetries at the core of environmental issues. Indeed, the understanding of regional water situations and social stumbling blocks needs not only to consider local capabilities and socio-political inequities, but also agro-industrial policy (e.i. cotton) and caste political alliances at a national scale, as well as ideological and narrative struggles or strategical orientations of financial backers at an international level. Our empirical research modestly contributes to the development of such a Political Ecology of water resources development and management.

Postnatal intracerebroventricular administrations of NGF alter spatial memory in adulthood

The present work assessed the effects of intracerebroventricular injections (2x5 mg/2.5 ml) of recombined human nerve growth factor (rhNGF) at postnatal days 2 and 3 upon the development of spatial learning capacities in rats. The treated rats were trained at the age of 22 days to escape onto an invisible platform at a fixed position in space in a Morris navigation task. For half of the subjects, the training position was also cued, a procedure aimed at facilitating escape and reducing attention to the distant spatial cues. At the age of 2 months all the rats were retrained in the same task. Treatment effects were found in both immature and adult rats. The injection of NGF induced a slight alteration of the immature rats' performance. In contrast, a marked impairment of spatial abilities was shown in the 2-month-old rats. The most consistent effects were a significant increase in the escape latency and a decrease bias towards the training platform area during probe trials. The reduction of spatial memory was particularly marked if the subjects had been trained in a cued condition. Taken together, these experiments reveal that an acute pharmacological treatment that leads to transient modifications during early development might induce a behavioural change long after treatment. Thus, the development and the maintenance of an accurate spatial representation are tightly related to the development of brain structures that could be altered by precocious NGF administrations.

Mapping the human connectome at multiple scales with diffusion spectrum MRI.

The global structural connectivity of the brain, the human connectome, is now accessible at millimeter scale with the use of MRI. In this paper, we describe an approach to map the connectome by constructing normalized whole-brain structural connection matrices derived from diffusion MRI tractography at 5 different scales. Using a template-based approach to match cortical landmarks of different subjects, we propose a robust method that allows (a) the selection of identical cortical regions of interest of desired size and location in different subjects with identification of the associated fiber tracts (b) straightforward construction and interpretation of anatomically organized whole-brain connection matrices and (c) statistical inter-subject comparison of brain connectivity at various scales. The fully automated post-processing steps necessary to build such matrices are detailed in this paper. Extensive validation tests are performed to assess the reproducibility of the method in a group of 5 healthy subjects and its reliability is as well considerably discussed in a group of 20 healthy subjects.

Spatial Scale of Clustering of Motor Vehicle Crash Types and Appropriate Countermeasures, 2009

This project analyzes the characteristics and spatial distributions of motor vehicle crash types in order to evaluate the degree and scale of their spatial clustering. Crashes occur as the result of a variety of vehicle, roadway, and human factors and thus vary in their clustering behavior. Clustering can occur at a variety of scales, from the intersection level, to the corridor level, to the area level. Conversely, other crash types are less linked to geographic factors and are more spatially “random.” The degree and scale of clustering have implications for the use of strategies to promote transportation safety. In this project, Iowa's crash database, geographic information systems, and recent advances in spatial statistics methodologies and software tools were used to analyze the degree and spatial scale of clustering for several crash types within the counties of the Iowa Northland Regional Council of Governments. A statistical measure called the K function was used to analyze the clustering behavior of crashes. Several methodological issues, related to the application of this spatial statistical technique in the context of motor vehicle crashes on a road network, were identified and addressed. These methods facilitated the identification of crash clusters at appropriate scales of analysis for each crash type. This clustering information is useful for improving transportation safety through focused countermeasures directly linked to crash causes and the spatial extent of identified problem locations, as well as through the identification of less location-based crash types better suited to non-spatial countermeasures. The results of the K function analysis point to the usefulness of the procedure in identifying the degree and scale at which crashes cluster, or do not cluster, relative to each other. Moreover, for many individual crash types, different patterns and processes and potentially different countermeasures appeared at different scales of analysis. This finding highlights the importance of scale considerations in problem identification and countermeasure formulation.

Confirmatory factor analysis of an integrated model of psycopathology assessed with MMPI-2-RF and the MCMI-III

We presented an integrated hierarchical model of psychopathology that more accurately captures empirical patterns of comorbidity between clinical syndromes and personality disorders.In order to verify the structural validity of the model proposed, this study aimed to analyze the convergence between the Restructured Clinical (RC) scales and Personality scales (PSY-5) of the MMPI-2-RF and the Clinical Syndrome and Personality Disorder scales of the MCMI-III.The MMPI-2-RF and MCMI-III were administered to a clinical sample of 377 outpatients (167 men and 210 women).The structural hypothesiswas assessed by using a Confirmatory Factor Analytic design with four common superordinate factors. An independent-cluster-basis solution was proposed based on maximum likelihood estimation and the application of several fit indices.The fit of the proposed model can be considered as good and more so if we take into account its complexity.

Dissociation between components of spatial memory in rats after recovery from the effects of retrohippocampal lesions

A series of 4 experiments examined the performance of rats with retrohippocampal lesions on a spatial water-maze task. The animals were trained to find and escape onto a hidden platform after swimming in a large pool of opaque water. The platform was invisible and could not be located using olfactory cues. Successful escape performance required the rats to develop strategies of approaching the correct location with reference solely to distal extramaze cues. The lesions encompassed the entire rostro-caudal extent of the lateral and medial entorhinal cortex, and included parts of the pre- and para-subiculum, angular bundle and subiculum. Groups ECR 1 and 2 sustained only partial damage of the subiculum, while Group ECR+S sustained extensive damage. These groups were compared with sham-lesion and unoperated control groups. In Expt 1A, a profound deficit in spatial localisation was found in groups ECR 1 and ECR+S, the rats receiving all training postoperatively. In Expt 1B, these two groups showed hyperactivity in an open-field. In Expt 2, extensive preoperative training caused a transitory saving in performance of the spatial task by group ECR 2, but comparisons with the groups of Expt 1A revealed no sustained improvement, except on one measure of performance in a post-training transfer test. All rats were then given (Expt 3) training on a cueing procedure using a visible platform. The spatial deficit disappeared but, on returning to the normal hidden platform procedure, it reappeared. Nevertheless, a final transfer test, during which the platform was removed from the apparatus, revealed a dissociation between two independent measures of performance: the rats with ECR lesions failed to search for the hidden platform but repeatedly crossed its correct location accurately during traverses of the entire pool. This partial recovery of performance was not (Expt 4) associated with any ability to discriminate between two locations in the pool. The apparently selective recovery of aspects of spatial memory is discussed in relation to O'Keefe and Nadel's (1978) spatial mapping theory of hippocampal function. We propose a modification of the theory in terms of a dissociation between procedural and declarative subcomponents of spatial memory. The declarative component is a flexible access system in which information is stored in a form independent of action. It is permanently lost after the lesion. The procedural component is "unmasked" by the retrohippocampal lesion giving rise to the partial recovery of spatial localisation performance.

Metabolic activation pattern of distinct hippocampal subregions during spatial learning and memory retrieval.

Activation dynamics of hippocampal subregions during spatial learning and their interplay with neocortical regions is an important dimension in the understanding of hippocampal function. Using the (14C)-2-deoxyglucose autoradiographic method, we have characterized the metabolic changes occurring in hippocampal subregions in mice while learning an eight-arm radial maze task. Autoradiogram densitometry revealed a heterogeneous and evolving pattern of enhanced metabolic activity throughout the hippocampus during the training period and on recall. In the early stages of training, activity was enhanced in the CA1 area from the intermediate portion to the posterior end as well as in the CA3 area within the intermediate portion of the hippocampus. At later stages, CA1 and CA3 activations spread over the entire longitudinal axis, while dentate gyrus (DG) activation occurred from the anterior to the intermediate zone. Activation of the retrosplenial cortex but not the amygdala was also observed during the learning process. On recall, only DG activation was observed in the same anterior part of the hippocampus. These results suggest the existence of a functional segmentation of the hippocampus, each subregion being dynamically but also differentially recruited along the acquisition, consolidation, and retrieval process in parallel with some neocortical sites.

Ibotenate Lesions of Hippocampus and/or Subiculum: Dissociating Components of Allocentric Spatial Learning

This study examined the effects of ibotenic acid-induced lesions of the hippocampus, subiculum and hippocampus +/- subiculum upon the capacity of rats to learn and perform a series of allocentric spatial learning tasks in an open-field water maze. The lesions were made by infusing small volumes of the neurotoxin at a total of 26 (hippocampus) or 20 (subiculum) sites intended to achieve complete target cell loss but minimal extratarget damage. The regional extent and axon-sparing nature of these lesions was evaluated using both cresyl violet and Fink - Heimer stained sections. The behavioural findings indicated that both the hippocampus and subiculum lesions caused impairment to the initial postoperative acquisition of place navigation but did not prevent eventual learning to levels of performance almost as effective as those of controls. However, overtraining of the hippocampus + subiculum lesioned rats did not result in significant place learning. Qualitative observations of the paths taken to find a hidden escape platform indicated that different strategies were deployed by hippocampal and subiculum lesioned groups. Subsequent training on a delayed matching to place task revealed a deficit in all lesioned groups across a range of sample choice intervals, but the subiculum lesioned group was less impaired than the group with the hippocampal lesion. Finally, unoperated control rats given both the initial training and overtraining were later given either a hippocampal lesion or sham surgery. The hippocampal lesioned rats were impaired during a subsequent retention/relearning phase. Together, these findings suggest that total hippocampal cell loss may cause a dual deficit: a slower rate of place learning and a separate navigational impairment. The prospect of unravelling dissociable components of allocentric spatial learning is discussed.

Prediction of soil orders with high spatial resolution: response of different classifiers to sampling density

The objective of this work was to evaluate sampling density on the prediction accuracy of soil orders, with high spatial resolution, in a viticultural zone of Serra Gaúcha, Southern Brazil. A digital elevation model (DEM), a cartographic base, a conventional soil map, and the Idrisi software were used. Seven predictor variables were calculated and read along with soil classes in randomly distributed points, with sampling densities of 0.5, 1, 1.5, 2, and 4 points per hectare. Data were used to train a decision tree (Gini) and three artificial neural networks: adaptive resonance theory, fuzzy ARTMap; self209;organizing map, SOM; and multi209;layer perceptron, MLP. Estimated maps were compared with the conventional soil map to calculate omission and commission errors, overall accuracy, and quantity and allocation disagreement. The decision tree was less sensitive to sampling density and had the highest accuracy and consistence. The SOM was the less sensitive and most consistent network. The MLP had a critical minimum and showed high inconsistency, whereas fuzzy ARTMap was more sensitive and less accurate. Results indicate that sampling densities used in conventional soil surveys can serve as a reference to predict soil orders in Serra Gaúcha.

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The quality of environmental data analysis and propagation of errors are heavily affected by the representativity of the initial sampling design [CRE 93, DEU 97, KAN 04a, LEN 06, MUL07]. Geostatistical methods such as kriging are related to field samples, whose spatial distribution is crucial for the correct detection of the phenomena. Literature about the design of environmental monitoring networks (MN) is widespread and several interesting books have recently been published [GRU 06, LEN 06, MUL 07] in order to clarify the basic principles of spatial sampling design (monitoring networks optimization) based on Support Vector Machines was proposed. Nonetheless, modelers often receive real data coming from environmental monitoring networks that suffer from problems of non-homogenity (clustering). Clustering can be related to the preferential sampling or to the impossibility of reaching certain regions.

Spatial predictions of land-use transitions and associated threats to biodiversity: the case of forest regrowth in mountain grasslands

Question Can we predict where forest regrowth caused by abandonment of agricultural activities is likely to occur? Can we assess how it may conflict with grassland diversity hotspots? Location Western Swiss Alps (4003210m a.s.l.). Methods We used statistical models to predict the location of land abandonment by farmers that is followed by forest regrowth in semi-natural grasslands of the Western Swiss Alps. Six modelling methods (GAM, GBM, GLM, RF, MDA, MARS) allowing binomial distribution were tested on two successive transitions occurring between three time periods. Models were calibrated using data on land-use change occurring between 1979 and 1992 as response, and environmental, accessibility and socio-economic variables as predictors, and these were validated for their capacity to predict the changes observed from 1992 to 2004. Projected probabilities of land-use change from an ensemble forecast of the six models were combined with a model of plant species richness based on a field inventory, allowing identification of critical grassland areas for the preservation of biodiversity. Results Models calibrated over the first land-use transition period predicted the second transition with reasonable accuracy. Forest regrowth occurs where cultivation costs are high and yield potential is low, i.e. on steeper slopes and at higher elevations. Overlaying species richness with land-use change predictions, we identified priority areas for the management and conservation of biodiversity at intermediate elevations. Conclusions Combining land-use change and biodiversity projections, we propose applied management measures for targeted/identified locations to limit the loss of biodiversity that could otherwise occur through loss of open habitats. The same approach could be applied to other types of land-use changes occurring in other ecosystems.