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.

Families of periodic orbits for the spatial isosceles 3-body problem

We study the families of periodic orbits of the spatial isosceles 3-body problem (for small enough values of the mass lying on the symmetry axis) coming via the analytic continuation method from periodic orbits of the circular Sitnikov problem. Using the first integral of the angular momentum, we reduce the dimension of the phase space of the problem by two units. Since periodic orbits of the reduced isosceles problem generate invariant two-dimensional tori of the nonreduced problem, the analytic continuation of periodic orbits of the (reduced) circular Sitnikov problem at this level becomes the continuation of invariant two-dimensional tori from the circular Sitnikov problem to the nonreduced isosceles problem, each one filled with periodic or quasi-periodic orbits. These tori are not KAM tori but just isotropic, since we are dealing with a three-degrees-of-freedom system. The continuation of periodic orbits is done in two different ways, the first going directly from the reduced circular Sitnikov problem to the reduced isosceles problem, and the second one using two steps: first we continue the periodic orbits from the reduced circular Sitnikov problem to the reduced elliptic Sitnikov problem, and then we continue those periodic orbits of the reduced elliptic Sitnikov problem to the reduced isosceles problem. The continuation in one or two steps produces different results. This work is merely analytic and uses the variational equations in order to apply Poincar´e’s continuation method.

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.

Central configurations of nested regular polyhedra for the spatial 2n–body problem

We consider 2n masses located at the vertices of two nested regular polyhedra with the same number of vertices. Assuming that the masses in each polyhedron are equal, we prove that for each ratio of the masses of the inner and the outer polyhedron there exists a unique ratio of the length of the edges of the inner and the outer polyhedron such that the configuration is central.

Central configurations of three nested regular polyhedra for the spatial 3n–body problem

Three regular polyhedra are called nested if they have the same number of vertices n, the same center and the positions of the vertices of the inner polyhedron ri, the ones of the medium polyhedron Ri and the ones of the outer polyhedron Ri satisfy the relation Ri = ri and Ri = Rri for some scale factors R > > 1 and for all i = 1, . . . , n. We consider 3n masses located at the vertices of three nested regular polyhedra. We assume that the masses of the inner polyhedron are equal to m1, the masses of the medium one are equal to m2, and the masses of the outer one are equal to m3. We prove that if the ratios of the masses m2/m1 and m3/m1 and the scale factors and R satisfy two convenient relations, then this configuration is central for the 3n–body problem. Moreover there is some numerical evidence that, first, fixed two values of the ratios m2/m1 and m3/m1, the 3n–body problem has a unique central configuration of this type; and second that the number of nested regular polyhedra with the same number of vertices forming a central configuration for convenient masses and sizes is arbitrary.

Spatial Polarization of the Ecological Footprint distribution

The international allocation of natural resources is determined, not by any ethical or ecological criteria, but by the dominance of market mechanisms. From a core-periphery perspective, this allocation may even be driven by historically determined structural patterns, with a core group of countries whose consumption appropriates most available natural resources, and another group, having low natural resource consumption, which plays a peripheral role. This article consists of an empirical distributional analysis of natural resource consumption (as measured by Ecological Footprints) whose purpose is to assess the extent to which the distribution of consumption responds to polarization (as opposed to mere inequality). To assess this, we estimate and decompose different polarization indices for a balanced sample of 119 countries over the period 1961 to 2007. Our results points toward a polarized distribution which is consistent with a core-periphery framework.

Organization and plasticity of auditory spatial representations

Spatial hearing refers to a set of abilities enabling us to determine the location of sound sources, redirect our attention toward relevant acoustic events, and recognize separate sound sources in noisy environments. Determining the location of sound sources plays a key role in the way in which humans perceive and interact with their environment. Deficits in sound localization abilities are observed after lesions to the neural tissues supporting these functions and can result in serious handicaps in everyday life. These deficits can, however, be remediated (at least to a certain degree) by the surprising capacity of reorganization that the human brain possesses following damage and/or learning, namely, the brain plasticity. In this thesis, our aim was to investigate the functional organization of auditory spatial functions and the learning-induced plasticity of these functions. Overall, we describe the results of three studies. The first study entitled "The role of the right parietal cortex in sound localization: A chronometric single pulse transcranial magnetic stimulation study" (At et al., 2011), study A, investigated the role of the right parietal cortex in spatial functions and its chronometry (i.e. the critical time window of its contribution to sound localizations). We concentrated on the behavioral changes produced by the temporarily inactivation of the parietal cortex with transcranial magnetic stimulation (TMS). We found that the integrity of the right parietal cortex is crucial for localizing sounds in the space and determined a critical time window of its involvement, suggesting a right parietal dominance for auditory spatial discrimination in both hemispaces. In "Distributed coding of the auditory space in man: evidence from training-induced plasticity" (At et al., 2013a), study B, we investigated the neurophysiological correlates and changes of the different sub-parties of the right auditory hemispace induced by a multi-day auditory spatial training in healthy subjects with electroencephalography (EEG). We report a distributed coding for sound locations over numerous auditory regions, particular auditory areas code specifically for precise parts of the auditory space, and this specificity for a distinct region is enhanced with training. In the third study "Training-induced changes in auditory spatial mismatch negativity" (At et al., 2013b), study C, we investigated the pre-attentive neurophysiological changes induced with a training over 4 days in healthy subjects with a passive mismatch negativity (MMN) paradigm. We showed that training changed the mechanisms for the relative representation of sound positions and not the specific lateralization themselves and that it changed the coding in right parahippocampal regions. - L'audition spatiale désigne notre capacité à localiser des sources sonores dans l'espace, de diriger notre attention vers les événements acoustiques pertinents et de reconnaître des sources sonores appartenant à des objets distincts dans un environnement bruyant. La localisation des sources sonores joue un rôle important dans la façon dont les humains perçoivent et interagissent avec leur environnement. Des déficits dans la localisation de sons sont souvent observés quand les réseaux neuronaux impliqués dans cette fonction sont endommagés. Ces déficits peuvent handicaper sévèrement les patients dans leur vie de tous les jours. Cependant, ces déficits peuvent (au moins à un certain degré) être réhabilités grâce à la plasticité cérébrale, la capacité du cerveau humain à se réorganiser après des lésions ou un apprentissage. L'objectif de cette thèse était d'étudier l'organisation fonctionnelle de l'audition spatiale et la plasticité induite par l'apprentissage de ces fonctions. Dans la première étude intitulé « The role of the right parietal cortex in sound localization : A chronometric single pulse study » (At et al., 2011), étude A, nous avons examiné le rôle du cortex pariétal droit dans l'audition spatiale et sa chronométrie, c'est-à- dire le moment critique de son intervention dans la localisation de sons. Nous nous sommes concentrés sur les changements comportementaux induits par l'inactivation temporaire du cortex pariétal droit par le biais de la Stimulation Transcrânienne Magnétique (TMS). Nous avons démontré que l'intégrité du cortex pariétal droit est cruciale pour localiser des sons dans l'espace. Nous avons aussi défini le moment critique de l'intervention de cette structure. Dans « Distributed coding of the auditory space : evidence from training-induced plasticity » (At et al., 2013a), étude B, nous avons examiné la plasticité cérébrale induite par un entraînement des capacités de discrimination auditive spatiale de plusieurs jours. Nous avons montré que le codage des positions spatiales est distribué dans de nombreuses régions auditives, que des aires auditives spécifiques codent pour des parties données de l'espace et que cette spécificité pour des régions distinctes est augmentée par l'entraînement. Dans « Training-induced changes in auditory spatial mismatch negativity » (At et al., 2013b), étude C, nous avons examiné les changements neurophysiologiques pré- attentionnels induits par un entraînement de quatre jours. Nous avons montré que l'entraînement modifie la représentation des positions spatiales entraînées et non-entrainées, et que le codage de ces positions est modifié dans des régions parahippocampales.

Maize yield and rainfall on different spatial and temporal scales in Southern Brazil

This study aimed to establish relationships between maize yield and rainfall on different temporal and spatial scales, in order to provide a basis for crop monitoring and modelling. A 16-year series of maize yield and daily rainfall from 11 municipalities and micro-regions of Rio Grande do Sul State was used. Correlation and regression analyses were used to determine associations between crop yield and rainfall for the entire crop cycle, from tasseling to 30 days after, and from 5 days before tasseling to 40 days after. Close relationships between maize yield and rainfall were found, particularly during the reproductive period (45-day period comprising the flowering and grain filling). Relationships were closer on a regional scale than at smaller scales. Implications of the crop-rainfall relationships for crop modelling are discussed.

Spatial and temporal regulation of " cdc16p " in the fission yeast " Schizosaccharomyces pombe "

Abstract: The fission yeast Schizosaccharomyces pombe has proven to be an excellent model system for the study of eukaryotic cell cycle control. S. pombe cells are rod-shaped and grow mainly by elongation at their tips. They divide by the means of a centrallyplaced division septum which provides two daughter cells of equal size. S. pombe cytokinesis begins at mitotic entry, when the division site is defined by formation of the contractile acto-myosin ring (CAR). Formation of the division septum is triggered at the end of mitosis by the spindle pole body (SPB) associated septation initiation network (SIN) proteins. SIN signalling requires activation of the GTPase spg1p, whose nucleotide status is regulated by the bipartite GAP byr4pcdc16p. Removal of cdc16p from the SPB during early mitosis is thought to allow priming of the SIN by association of cdc7p with both SPBs. During anaphase cdc7p is retained on the new SPB, which also recruits the kinase sid1 p and cdc14p, while the old SP8 reassembles the byr4-cdc16p GAP and is presumed not to signal; SPB asymmetry persists throughout anaphase. The trigger for inactivation of SIN signalling at the new SPB is unknown. This study has concentrated upon cdc16p. We have undertaken the analysis of the localisation of cdc16p using time-lapse microscopy. We have observed that the localisation of cdc16p is regulated at different transitions. We have shown that cdc16p is removed from the SPB prior to the onset of spindle formation and that it reappears asymmetrically at the beginning of anaphase B. We have also demonstrated that the resetting of the SIN at the new SPB is linked to completion of CAR contraction and septum formation. We propose the existence of a mechanism that monitors cytokinesis and that couples the activity of the SI N with the presence of the CAR. During the biochemical characterization of cdc16p, We have found that it is an unstable protein and that it is subjected to polyubiquitination by the SCF and proteasomal degradation. Together, these observations help to shed new light upon the mechanisms by which cytokinesis is regulated in S. pombe. Résumé: La levure Schizosaccharomyces pombe est un excellent organisme modèle pour l'étude du cycle cellulaire eucaryote. Les cellules S. pombe ont la forme de bâtonnets et croissent par l'allongement de leurs extrémités. Elles se divisent en formant, en leur milieu une paroi cellulaire, appelé septum, permettant ainsi l'obtention de deux cellules filles de même taille. Chez S. pombe, la cytokinèse commence en début de mitose lorsque le site de division est déterminé par la formation d'un anneau d'acto-myosine. Le septum, lui, est formé uniquement en fin de mitose par la contraction de l'anneau d'actomyosine. Cette contraction est sous le contrôle d'un réseau de signalisation cellulaire appelé le «réseau d'initiation de synthèse du septum » ou « septation initiation network » (SIN), qui se situe sur les pôles du fuseau mitotique. L'activation du SIN dépend d'une GTPase appelé spg1p dont le statut nucléotidique dépend des protéines cdclóp et byr4p qui forment un complexe qui favorise l'hydrolyse du GTP en GDP. En début de mitose, cdc16p ne se situe plus sur les poles du fuseau mitotique. La GTPase spg1p se retrouve donc principalement sous sa forme couplée au GTP, ce quí va permettre son interaction avec la kinase cdc7p. Cette protéine ainsi que deux autres kinases sid2p (avec mob1p) et sid1p (avec cdc14p) permettent la transmission du signal d'initiation de la contraction de l'anneau d'acto-myosine en fin d'anaphase. Pendant l'anaphase, cdc7p, sid1 p et cdc14p localisent sur un des deux pôles du fuseau mitotique. Il en est de même pour cdc1p et by14p et le pôle contenant cdc16p et byr4p est toujours différent de celui ou les régulateurs positifs du SIN se situent. En fin de cytokinèse, cdc16 et byr4p se retrouvent à nouveau sur chaque pôle des deux cellules filles. Dans cette étude, nous nous sommes concentrés sur l'analyse de la localisation de cdc16p pendant la mitose en utilisant une technique de microscopie en temps réel. Nous avons été en mesure de déterminer que le départ de cdc16p du pole s'effectue juste avant la formation du fuseau mitotique. Nous avons aussi découvert que la localisation asymétrique des composants du SIN dépend fortement de l'entrée en anaphase B. Finalement, Nous avons montré que distribution asymétrique des composants du SIN sur les pôles du fuseau mitotique dépendait aussi fortement de !a présence de l'anneau d'acto-myosine. Ceci nous permet donc de proposer l'existence d'un mécanisme cellulaire qui permet de s'assurer que la cytokinèse est achevée avant de diminuer la signalisation du SIN. Par ailleurs, des études biochimiques nous ont permis de montrer que cdc16p est dégradé par le proteosome. Ces travaux ont permis la découverte de nouveaux modes de régulation du SIN.

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.

Protease modulation of the activity of the epithelial sodium channel expressed in Xenopus oocytes.

We have investigated the effect of extracellular proteases on the amiloride-sensitive Na+ current (INa) in Xenopus oocytes expressing the three subunits alpha, beta, and gamma of the rat or Xenopus epithelial Na+ channel (ENaC). Low concentrations of trypsin (2 microg/ml) induced a large increase of INa within a few minutes, an effect that was fully prevented by soybean trypsin inhibitor, but not by amiloride. A similar effect was observed with chymotrypsin, but not with kallikrein. The trypsin-induced increase of INa was observed with Xenopus and rat ENaC, and was very large (approximately 20-fold) with the channel obtained by coexpression of the alpha subunit of Xenopus ENaC with the beta and gamma subunits of rat ENaC. The effect of trypsin was selective for ENaC, as shown by the absence of effect on the current due to expression of the K+ channel ROMK2. The effect of trypsin was not prevented by intracellular injection of EGTA nor by pretreatment with GTP-gammaS, suggesting that this effect was not mediated by G proteins. Measurement of the channel protein expression at the oocyte surface by antibody binding to a FLAG epitope showed that the effect of trypsin was not accompanied by an increase in the channel protein density, indicating that proteolysis modified the activity of the channel present at the oocyte surface rather than the cell surface expression. At the single channel level, in the cell-attached mode, more active channels were observed in the patch when trypsin was present in the pipette, while no change in channel activity could be detected when trypsin was added to the bath solution around the patch pipette. We conclude that extracellular proteases are able to increase the open probability of the epithelial sodium channel by an effect that does not occur through activation of a G protein-coupled receptor, but rather through proteolysis of a protein that is either a constitutive part of the channel itself or closely associated with it.

Ectodysplasin A (EDA) - EDA receptor signalling and its pharmacological modulation.

The TNF family ligand ectodysplasin A (EDA) regulates the induction, morphogenesis and/or maintenance of skin-derived structures such as teeth, hair, sweat glands and several other glands. Deficiencies in the EDA - EDA receptor (EDAR) signalling pathway cause hypohidrotic ectodermal dysplasia (HED). This syndrome is characterized by the absence or malformation of several skin-derived appendages resulting in hypotrychosis, hypodontia, heat-intolerance, dry skin and dry eyes, susceptibility to airways infections and crusting of various secretions. The EDA-EDAR system is an important effector of canonical Wnt signalling in developing skin appendages. It functions by stimulating NF-κB-mediated transcription of effectors or inhibitors of the Wnt, Sonic hedgehog (SHH), fibroblast growth factor (FGF) and transforming growth factor beta (TGFβ) pathways that regulate interactions within or between epithelial and mesenchymal cells and tissues. In animal models of Eda-deficiency, soluble EDAR agonists can precisely correct clinically relevant symptoms with low side effects even at high agonist doses, indicating that efficient negative feedback signals occur in treated tissues. Hijacking of the placental antibody transport system can help deliver active molecules to developing foetuses in a timely manner. EDAR agonists may serve to treat certain forms of ectodermal dysplasia.

Working memory in schizophrenia: dynamic visuo-spatial information processing

Working memory, commonly defined as the ability to hold mental representations on line transiently and to manipulate these representations, is known to be a core deficit in schizophrenia. The aim of the present study was to investigate the visuo-spatial component of the working memory in schizophrenia, and more precisely to what extent the dynamic visuo-spatial information processing is impaired in schizophrenia patients. For this purpose we used a computerized paradigm in which 29 patients with schizophrenia (DSMIV, Diagnostic Interview for Genetic Studies) and 29 age and sex matched control subjects (DIGS) had to memorize a plane moving across the computer screen and to identify the observed trajectory among 9 plots proposed together. Each trajectory could be seen max. 3 times if needed. The results showed no difference between schizophrenia patients and controls regarding the number of correct trajectory identified after the first presentation. However, when we determine the mean number of correct trajectories on the basis of 3 trials, we observed that schizophrenia patients are significantly less performant than controls (Mann-Whitney, p _ 0.002). These findings suggest that, although schizophrenia patients are able to memorize some dynamic trajectories as well as controls, they do not profit from the repetition of the trajectory presentation. These findings are congruent with the hypothesis that schizophrenia could induce an unbalance between local and global information processing: the patients may be able to focus on details of the trajectory which could allow them to find the right target (bottom-up processes), but may show difficulty to refer to previous experience in order to filter incoming information (top-down processes) and enhance their visuo-spatial working memory abilities.

Computed tomography commissioning programmes: how to obtain a reliable MTF with an automatic approach?

The purpose of this study was to assess the spatial resolution of a computed tomography (CT) scanner with an automatic approach developed for routine quality controls when varying CT parameters. The methods available to assess the modulation transfer functions (MTF) with the automatic approach were Droege's and the bead point source (BPS) methods. These MTFs were compared with presampled ones obtained using Boone's method. The results show that Droege's method is not accurate in the low-frequency range, whereas the BPS method is highly sensitive to image noise. While both methods are well adapted to routine stability controls, it was shown that they are not able to provide absolute measurements. On the other hand, Boone's method, which is robust with respect to aliasing, more resilient to noise and provides absolute measurements, satisfies the commissioning requirements perfectly. Thus, Boone's method combined with a modified Catphan 600 phantom could be a good solution to assess CT spatial resolution in the different CT planes.