GeoKernels: Modeling of Spatial Data on GeoManifolds

This paper presents a review of methodology for semi-supervised modeling with kernel methods, when the manifold assumption is guaranteed to be satisfied. It concerns environmental data modeling on natural manifolds, such as complex topographies of the mountainous regions, where environmental processes are highly influenced by the relief. These relations, possibly regionalized and nonlinear, can be modeled from data with machine learning using the digital elevation models in semi-supervised kernel methods. The range of the tools and methodological issues discussed in the study includes feature selection and semisupervised Support Vector algorithms. The real case study devoted to data-driven modeling of meteorological fields illustrates the discussed approach.

Effects of pro-cholinergic treatment in patients suffering from spatial neglect.

Spatial neglect is a neurological condition characterized by a breakdown of spatial cognition contralateral to hemispheric damage. Deficits in spatial attention toward the contralesional side are considered to be central to this syndrome. Brain lesions typically involve right fronto-parietal cortices mediating attentional functions and subcortical connections in underlying white matter. Convergent findings from neuroimaging and behavioral studies in both animals and humans suggest that the cholinergic system might also be critically implicated in selective attention by modulating cortical function via widespread projections from the basal forebrain. Here we asked whether deficits in spatial attention associated with neglect could partly result from a cholinergic deafferentation of cortical areas subserving attentional functions, and whether such disturbances could be alleviated by pro-cholinergic therapy. We examined the effect of a single-dose transdermal nicotine treatment on spatial neglect in 10 stroke patients in a double-blind placebo-controlled protocol, using a standardized battery of neglect tests. Nicotine-induced systematic improvement on cancellation tasks and facilitated orienting to single visual targets, but had no significant effect on other tests. These results support a global effect of nicotine on attention and arousal, but no effect on other spatial mechanisms impaired in neglect.

Dispersal strategies, few dominating or many coexisting: the effect of environmental spatial structure and multiple sources of mortality.

Interspecific competition, life history traits, environmental heterogeneity and spatial structure as well as disturbance are known to impact the successful dispersal strategies in metacommunities. However, studies on the direction of impact of those factors on dispersal have yielded contradictory results and often considered only few competing dispersal strategies at the same time. We used a unifying modeling approach to contrast the combined effects of species traits (adult survival, specialization), environmental heterogeneity and structure (spatial autocorrelation, habitat availability) and disturbance on the selected, maintained and coexisting dispersal strategies in heterogeneous metacommunities. Using a negative exponential dispersal kernel, we allowed for variation of both species dispersal distance and dispersal rate. We showed that strong disturbance promotes species with high dispersal abilities, while low local adult survival and habitat availability select against them. Spatial autocorrelation favors species with higher dispersal ability when adult survival and disturbance rate are low, and selects against them in the opposite situation. Interestingly, several dispersal strategies coexist when disturbance and adult survival act in opposition, as for example when strong disturbance regime favors species with high dispersal abilities while low adult survival selects species with low dispersal. Our results unify apparently contradictory previous results and demonstrate that spatial structure, disturbance and adult survival determine the success and diversity of coexisting dispersal strategies in competing metacommunities.

Spatial pattern of floral morphology: a possible insight into the effects of pollinators on plant distribution

Pollination syndromes involve convergent evolution towards phenotypes composed of specific scents, colours or floral morphologies that attract or restrict pollinator access to reward. How these traits might influence the distributions of plant species in interaction with pollinators has rarely been investigated. We sampled 870 vegetation plots in the western Swiss Alps and classified the plant species into seven blossom types according to their floral morphology (wind, disk, funnel, tube, bilabiate, head or brush). We investigated the environmental features of plots with functional diversity (FD) lower than expected by chance alone to detect potential pollination filtering and related the proportions of the seven blossom types to a combination of environmental descriptors. From these results, we inferred the potential effect of the pollinator on the spatial distribution of plant species. The vegetation plots with significantly lower FD of blossom types than expected by chance were found at higher altitudes, and the proportions of blossom types were strongly patterned along the same gradient. These results support a biotic filtering effect on plant species assemblages through pollination: disk blossoms became dominant at higher altitudes, resulting in a lower FD. In harsh conditions at high altitudes, pollinators usually decrease in activity, and the openness of the disk blossom grants access to any available pollinator. Inversely, bilabiate blossoms, which are mostly pollinated by bees, were more abundant at lower elevations, which are characterised by greater abundance and diversity of bees. Generalisation through openness of the blossom could be advantageous at high elevations, while specialisation could be a successful alternative strategy at lower elevations. The approach used in this study is purely correlative, and further investigations should be conducted to infer the nature of the causal relationship between plant and pollinator distributions.

Testing Spatial Autocorrelation in Weighted Networks : the Modes Permutation Test

In a weighted spatial network, as specified by an exchange matrix, the variances of the spatial values are inversely proportional to the size of the regions. Spatial values are no more exchangeable under independence, thus weakening the rationale for ordinary permutation and bootstrap tests of spatial autocorrelation. We propose an alternative permutation test for spatial autocorrelation, based upon exchangeable spatial modes, constructed as linear orthogonal combinations of spatial values. The coefficients obtain as eigenvectors of the standardised exchange matrix appearing in spectral clustering, and generalise to the weighted case the concept of spatial filtering for connectivity matrices. Also, two proposals aimed at transforming an acessibility matrix into a exchange matrix with with a priori fixed margins are presented. Two examples (inter-regional migratory flows and binary adjacency networks) illustrate the formalism, rooted in the theory of spectral decomposition for reversible Markov chains.

Combined analysis of grey matter voxel-based morphometry and white matter tract-based spatial statistics in late-life bipolar disorder.

Background: Previous magnetic resonance imaging (MRI) studies in young patients with bipolar disorder indicated the presence of grey matter concentration changes as well as microstructural alterations in white matter in various neocortical areas and the corpus callosum. Whether these structural changes are also present in elderly patients with bipolar disorder with long-lasting clinical evolution remains unclear. Methods: We performed a prospective MRI study of consecutive elderly, euthymic patients with bipolar disorder and healthy, elderly controls. We conducted a voxel-based morphometry (VBM) analysis and a tract-based spatial statistics (TBSS) analysis to assess fractional anisotropy and longitudinal, radial and mean diffusivity derived by diffusion tensor imaging (DTI). Results: We included 19 patients with bipolar disorder and 47 controls in our study. Fractional anisotropy was the most sensitive DTI marker and decreased significantly in the ventral part of the corpus callosum in patients with bipolar disorder. Longitudinal, radial and mean diffusivity showed no significant between-group differences. Grey matter concentration was reduced in patients with bipolar disorder in the right anterior insula, head of the caudate nucleus, nucleus accumbens, ventral putamen and frontal orbital cortex. Conversely, there was no grey matter concentration or fractional anisotropy increase in any brain region in patients with bipolar disorder compared with controls. Limitations: The major limitation of our study is the small number of patients with bipolar disorder. Conclusion: Our data document the concomitant presence of grey matter concentration decreases in the anterior limbic areas and the reduced fibre tract coherence in the corpus callosum of elderly patients with long-lasting bipolar disorder.

Improving generalized regression analysis for the spatial prediction of forest communities

Aim This study used data from temperate forest communities to assess: (1) five different stepwise selection methods with generalized additive models, (2) the effect of weighting absences to ensure a prevalence of 0.5, (3) the effect of limiting absences beyond the environmental envelope defined by presences, (4) four different methods for incorporating spatial autocorrelation, and (5) the effect of integrating an interaction factor defined by a regression tree on the residuals of an initial environmental model. Location State of Vaud, western Switzerland. Methods Generalized additive models (GAMs) were fitted using the grasp package (generalized regression analysis and spatial predictions, http://www.cscf.ch/grasp). Results Model selection based on cross-validation appeared to be the best compromise between model stability and performance (parsimony) among the five methods tested. Weighting absences returned models that perform better than models fitted with the original sample prevalence. This appeared to be mainly due to the impact of very low prevalence values on evaluation statistics. Removing zeroes beyond the range of presences on main environmental gradients changed the set of selected predictors, and potentially their response curve shape. Moreover, removing zeroes slightly improved model performance and stability when compared with the baseline model on the same data set. Incorporating a spatial trend predictor improved model performance and stability significantly. Even better models were obtained when including local spatial autocorrelation. A novel approach to include interactions proved to be an efficient way to account for interactions between all predictors at once. Main conclusions Models and spatial predictions of 18 forest communities were significantly improved by using either: (1) cross-validation as a model selection method, (2) weighted absences, (3) limited absences, (4) predictors accounting for spatial autocorrelation, or (5) a factor variable accounting for interactions between all predictors. The final choice of model strategy should depend on the nature of the available data and the specific study aims. Statistical evaluation is useful in searching for the best modelling practice. However, one should not neglect to consider the shapes and interpretability of response curves, as well as the resulting spatial predictions in the final assessment.

Mandatory communication skills training for oncologists: enforcement does not substantially impact satisfaction.

PURPOSE: Even though there is evidence that both patients and oncology clinicians are affected by the quality of communication and that communication skills can be effectively trained, so-called Communication Skills Trainings (CSTs) remain heterogeneously implemented. METHODS: A systematic evaluation of the level of satisfaction of oncologists with the Swiss CST before (2000-2005) and after (2006-2012) it became mandatory. RESULTS: Levels of satisfaction with the CST were high, and satisfaction of physicians participating on a voluntary or mandatory basis did not significantly differ for the majority of the items. CONCLUSIONS: The evaluation of physicians' satisfaction over the years and after introduction of mandatory training supports recommendations for generalized implementation of CST and mandatory training for medical oncologists.

Measuring ecological niche overlap from occurrence and spatial environmental data

1. Aim - Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data.¦2. Location - Europe, North America, South America¦3. Methods - The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with predefined distributions and amounts of niche overlap to evaluate several ordination and species distribution modeling techniques for quantifying niche overlap. We illustrate the approach with data on two well-studied invasive species.¦4. Results - We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographic space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results.¦5. Main conclusions - The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate to study niche differences between species, subspecies or intraspecific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intraspecific lineage has changed over time.

Tracking individuals shows spatial fidelity is a key regulator of ant social organization.

Ants live in organized societies with a marked division of labor among workers, but little is known about how this division of labor is generated. We used a tracking system to continuously monitor individually tagged workers in six colonies of the ant Camponotus fellah over 41 days. Network analyses of more than 9 million interactions revealed three distinct groups that differ in behavioral repertoires. Each group represents a functional behavioral unit with workers moving from one group to the next as they age. The rate of interactions was much higher within groups than between groups. The precise information on spatial and temporal distribution of all individuals allowed us to calculate the expected rates of within- and between-group interactions. These values suggest that the network of interaction within colonies is primarily mediated by age-induced changes in the spatial location of workers.

Habiter touristique et agencement de l'espace urbain : le cas de Los Angeles : recherche sur le concours des compétences des individus quant à leurs manières de faire avec les épreuves spatiales d'une métapole touristique

Vivre, c'est passer d'un espace à un autre en essayant le plus possible de ne pas se cogner déclamait George Pérec. Cet énoncé poétiquement géographique pourrait résumer d'une certaine façon le défi de connaissance saisi par cette recherche. L'enjeu consiste effectivement à envisager le fait à'habiter, entendu dans son acception du « faire avec de l'espace » de la part des individus, comme n'allant pas de soi, de mettre en exergue le caractère problématique que constitue la pratique d'un lieu pour un individu. A ce titre, l'une des propositions de ce travail est de considérer tout lieu comme un assemblage d'épreuves spatiales face auxquelles les individus sont confrontés. La question se pose alors de savoir comment les individus font avec ces épreuves spatiales. L'hypothèse défendue dans ce travail est celle de la mobilisation, par ces derniers, de compétences - ressortissant d'une « capacité à » telle qu'exprimée par Wittgenstein dans le domaine linguistique, c'est-à-dire d'une « maîtrise technique » - et d'un capital spatial - que l'on peut faire synthétiquement correspondre à l'expérience accumulée par un individu en terme de pratique de lieux. L'argumentation étaye l'hypothèse que les manières d'habiter touristiquement une métropole dépendent notamment de ces deux éléments interdépendants dont dispose tout individu de façon variable et évolutive ; leur importance, sans déterminer aucunement des pratiques spécifiques, participe d'une maîtrise accrue de l'espace, d'une facilité pour faire avec les épreuves spatiales, atténuant le caractère potentiellement contraignant de ces dernières. Il s'agit donc d'une enquête menant une réflexion tout à la fois sur la dimension actorielle des individus, mais également sur le lieu en tant qu'espace habité : travailler sur cette question revient à investir la question de l'agencement urbain d'un lieu, c'est-à-dire d'appréhender la façon dont une configuration urbaine (les épreuves spatiales coïncidant avec les principales caractéristiques de cette dernière) est habitée, et plus particulièrement en l'occurrence ici, est habitée touristiquement. Pour aborder empiriquement cette problématique, l'enquête se focalise donc sur les touristes : d'une part pour leur faible degré de familiarité avec le lieu pratiqué (faire avec cet espace ne relève donc pas d'une routine) et d'autre part parce que leur présence dorénavant massive au sein des métropoles a des effets sur l'agencement de ces lieux qu'il est nécessaire d'envisager. Le laboratoire utilisé est celui de Los Angeles, cette aire urbaine de 18 millions de résidents : son étalement considérable, l'absence d'un centre-ville historiquement important, et la forte prégnance de sa métrique automobile étant des caractéristiques qui font de ce lieu un « exceptionnel normal » aux épreuves spatiales particulièrement proéminentes. La recherche avance à ce titre des arguments permettant d'en souligner un agencement, par les manières d'habiter des touristes, différencié du modèle classique de la métropole touristique : pour exprimer cette singularité, l'enquête étaye l'hypothèse consistant à qualifier ce lieu de métapole touristique. - Living is moving from one space to another while trying not to collide claimed George Pérec. This poetically geographic statement could in a way sum up the challenge seized by this research. The challenge is indeed to consider the fact of dwelling, in the sense of "make do with space" on the part of individuals, as not an evidence but highlighting the problematic characteristics of the practice of a place by people. Accordingly, one of the proposals of this work is to consider each place as a gathering of spatial stakes against which individuals are faced. The question then arises how are individuals facing these spatial stakes. The hypothesis debated in this work is that of the mobilization of skills such as "the ability of' as expressed by Wittgenstein in the linguistic field, i.e. a "technical mastery" - and a spatial capital - that can synthetically correspond to the experience accumulated by one single individual in terms of practice of places. Argument supports the hypothesis that the ways of touristically dwelling a metropolis depend on these two interdependent elements which everyone deal with in a variable and scalable manner; their importance, without determining any specific practices, participates in an increased proficiency of space, easing to make do with the space stakes, moderating the potentially binding character of the latter. It is therefore a survey leading a reflection both on the actorial dimension of individuals, but also on the place as a living space: working on this issue is exploring the question of the urban layout of a place, i.e. to understand how an urban configuration (the space stakes coinciding with the main features of the latter) is inhabited, and in particular in the present case, is touristically dwelled. To empirically address this issue, the inquiry therefore focuses on tourists: on the one hand for their low degree of familiarity with the place (make do with this space is therefore not a routine) and secondly because their now massive presence within the metropolis has effects on the layout of these places that is necessary to consider. The laboratory used is that of Los Angeles, this urban area of 18 million residents: its considerable spread, the absence of an historically important downtown» and high salience of "automobile metric" are features that make this place a "normal exceptional" with particularly prominent space stakes. Hence, research advances the arguments underlining the layout, by the ways of tourists dwelling different from the classical model of the metropolis: to express this uniqueness, the survey supports hypothesis to describe this place as a tourist metapolis.

Food's visually perceived fat content affects discrimination speed in an orthogonal spatial task.

Choosing what to eat is a complex activity for humans. Determining a food's pleasantness requires us to combine information about what is available at a given time with knowledge of the food's palatability, texture, fat content, and other nutritional information. It has been suggested that humans may have an implicit knowledge of a food's fat content based on its appearance; Toepel et al. (Neuroimage 44:967-974, 2009) reported visual-evoked potential modulations after participants viewed images of high-energy, high-fat food (HF), as compared to viewing low-fat food (LF). In the present study, we investigated whether there are any immediate behavioural consequences of these modulations for human performance. HF, LF, or non-food (NF) images were used to exogenously direct participants' attention to either the left or the right. Next, participants made speeded elevation discrimination responses (up vs. down) to visual targets presented either above or below the midline (and at one of three stimulus onset asynchronies: 150, 300, or 450 ms). Participants responded significantly more rapidly following the presentation of a HF image than following the presentation of either LF or NF images, despite the fact that the identity of the images was entirely task-irrelevant. Similar results were found when comparing response speeds following images of high-carbohydrate (HC) food items to low-carbohydrate (LC) food items. These results support the view that people rapidly process (i.e. within a few hundred milliseconds) the fat/carbohydrate/energy value or, perhaps more generally, the pleasantness of food. Potentially as a result of HF/HC food items being more pleasant and thus having a higher incentive value, it seems as though seeing these foods results in a response readiness, or an overall alerting effect, in the human brain.

The role of phylogeny in the spatial distributions and assembly of mountain plant communities.

A major challenge in community ecology is a thorough understanding of the processes that govern the assembly and composition of communities in time and space. The growing threat of climate change to the vascular plant biodiversity of fragile ecosystems such as mountains has made it equally imperative to develop comprehensive methodologies to provide insights into how communities are assembled. In this perspective, the primary objective of this PhD thesis is to contribute to the theoretical and methodological development of community ecology, by proposing new solutions to better detect the ecological and evolutionary processes that govern community assembly. As phylogenetic trees provide by far, the most advanced tools to integrate the spatial, ecological and evolutionary dynamics of plant communities, they represent the cornerstone on which this work was based. In this thesis, I proposed new solutions to: (i) reveal trends in community assembly on phylogenies, depicted by the transition of signals at the nodes of the different species and lineages responsible for community assembly, (ii) contribute to evidence the importance of evolutionarily labile traits in the distribution of mountain plant species. More precisely, I demonstrated that phylogenetic and functional compositional turnover in plant communities was driven by climate and human land use gradients mostly influenced by evolutionarily labile traits, (iii) predict and spatially project the phylogenetic structure of communities using species distribution models, to identify the potential distribution of phylogenetic diversity, as well as areas of high evolutionary potential along elevation. The altitudinal setting of the Diablerets mountains (Switzerland) provided an appropriate model for this study. The elevation gradient served as a compression of large latitudinal variations similar to a collection of islands within a single area, and allowed investigations on a large number of plant communities. Overall, this thesis highlights that stochastic and deterministic environmental filtering processes mainly influence the phylogenetic structure of plant communities in mountainous areas. Negative density-dependent processes implied through patterns of phylogenetic overdispersion were only detected at the local scale, whereas environmental filtering implied through phylogenetic clustering was observed at both the regional and local scale. Finally, the integration of indices of phylogenetic community ecology with species distribution models revealed the prospects of providing novel and insightful explanations on the potential distribution of phylogenetic biodiversity in high mountain areas. These results generally demonstrate the usefulness of phylogenies in inferring assembly processes, and are worth considering in the theoretical and methodological development of tools to better understand phylogenetic community structure.

Weight status and gender-related differences in motor skills and in child care - based physical activity in young children.

Over the last decades, a decline in motor skills and in physical activity and an increase in obesity has been observed in children. However, there is a lack of data in young children. We tested if differences in motor skills and in physical activity according to weight or gender were already present in 2- to 4-year-old children. Fifty-eight child care centers in the French part of Switzerland were randomly selected for the Youp'là bouge study. Motor skills were assessed by an obstacle course including 5 motor skills, derived from the Zurich Neuromotor Assessment test. Physical activity was measured with accelerometers (GT1M, Actigraph, Florida, USA) using age-adapted cut-offs. Weight status was assessed using the International Obesity Task Force criteria (healthy weight vs overweight) for body mass index (BMI). Of the 529 children (49% girls, 3.4 ± 0.6 years, BMI 16.2 ± 1.2 kg/m2), 13% were overweight. There were no significant weight status-related differences in the single skills of the obstacle course, but there was a trend (p = 0.059) for a lower performance of overweight children in the overall motor skills score. No significant weight status-related differences in child care-based physical activity were observed. No gender-related differences were found in the overall motor skills score, but boys performed better than girls in 2 of the 5 motor skills (p ≤ 0.04). Total physical activity as well as time spent in moderate-vigorous and in vigorous activity during child care were 12-25% higher and sedentary activity 5% lower in boys compared to girls (all p < 0.01). At this early age, there were no significant weight status- or gender-related differences in global motor skills. However, in accordance to data in older children, child care-based physical activity was higher in boys compared to girls. These results are important to consider when establishing physical activity recommendations or targeting health promotion interventions in young children.

Understanding the ecological niche to elucidate spatial strategies of the southernmost Tupinambis lizards

Understanding factors that shape ranges of species is central in evolutionary biology. Species distribution models have become important tools to test biogeographical, ecological and evolutionary hypotheses. Moreover, from an ecological and evolutionary perspective, these models help to elucidate the spatial strategies of species at a regional scale. We modelled species distributions of two phylogenetically, geographically and ecologically close Tupinambis species (Teiidae) that occupy the southernmost area of the genus distribution in South America. We hypothesized that similarities between these species might have induced spatial strategies at the species level, such as niche differentiation and divergence of distribution patterns at a regional scale. Using logistic regression and MaxEnt we obtained species distribution models that revealed interspecific differences in habitat requirements, such as environmental temperature, precipitation and altitude. Moreover, the models obtained suggest that although the ecological niches of Tupinambis merianae and T. rufescens are different, these species might co-occur in a large contact zone. We propose that niche plasticity could be the mechanism enabling their co-occurrence. Therefore, the approach used here allowed us to understand the spatial strategies of two Tupinambis lizards at a regional scale.