Predicting the connectivity of primate cortical networks from topological and spatial node properties

Abstract Background The organization of the connectivity between mammalian cortical areas has become a major subject of study, because of its important role in scaffolding the macroscopic aspects of animal behavior and intelligence. In this study we present a computational reconstruction approach to the problem of network organization, by considering the topological and spatial features of each area in the primate cerebral cortex as subsidy for the reconstruction of the global cortical network connectivity. Starting with all areas being disconnected, pairs of areas with similar sets of features are linked together, in an attempt to recover the original network structure. Results Inferring primate cortical connectivity from the properties of the nodes, remarkably good reconstructions of the global network organization could be obtained, with the topological features allowing slightly superior accuracy to the spatial ones. Analogous reconstruction attempts for the C. elegans neuronal network resulted in substantially poorer recovery, indicating that cortical area interconnections are relatively stronger related to the considered topological and spatial properties than neuronal projections in the nematode. Conclusion The close relationship between area-based features and global connectivity may hint on developmental rules and constraints for cortical networks. Particularly, differences between the predictions from topological and spatial properties, together with the poorer recovery resulting from spatial properties, indicate that the organization of cortical networks is not entirely determined by spatial constraints.

Spatio-temporal patterns of tuberculosis incidence in Ribeirão Preto, State of São Paulo, southeast Brazil, and their relationship with social vulnerability: a Bayesian analysis

INTRODUCTION: The purpose of this ecological study was to evaluate the urban spatial and temporal distribution of tuberculosis (TB) in Ribeirão Preto, State of São Paulo, southeast Brazil, between 2006 and 2009 and to evaluate its relationship with factors of social vulnerability such as income and education level. METHODS: We evaluated data from TBWeb, an electronic notification system for TB cases. Measures of social vulnerability were obtained from the SEADE Foundation, and information about the number of inhabitants, education and income of the households were obtained from Brazilian Institute of Geography and Statistics. Statistical analyses were conducted by a Bayesian regression model assuming a Poisson distribution for the observed new cases of TB in each area. A conditional autoregressive structure was used for the spatial covariance structure. RESULTS: The Bayesian model confirmed the spatial heterogeneity of TB distribution in Ribeirão Preto, identifying areas with elevated risk and the effects of social vulnerability on the disease. We demonstrated that the rate of TB was correlated with the measures of income, education and social vulnerability. However, we observed areas with low vulnerability and high education and income, but with high estimated TB rates. CONCLUSIONS: The study identified areas with different risks for TB, given that the public health system deals with the characteristics of each region individually and prioritizes those that present a higher propensity to risk of TB. Complex relationships may exist between TB incidence and a wide range of environmental and intrinsic factors, which need to be studied in future research.

Estabilidade temporal e variabilidade espacial da distribuição da armazenagem de água no solo numa sucessão feijão/aveia-preta

A armazenagem de água no solo é muito variável no tempo e no espaço devido à influência de vários fatores ambientais e topográficos. Objetivou-se neste estudo: quantificar a armazenagem de água no solo; avaliar sua estabilidade temporal e sua variabilidade espacial em um local próximo e outro distante do sistema radicular numa sucessão feijão/aveia-preta; e constatar sua variabilidade espacial em função do relevo. Em área experimental de 1.500 m², situada em Piracicaba-SP (latitude de 22° 42' 30" S, longitude de 47° 38' 00" W e 546 m de altitude), estabeleceram-se 60 pontos de amostragem, distanciados entre si de 5 m, numa grade de 10 por 6 pontos (50 x 30 m). Os valores da armazenagem de água no solo apresentaram comportamento-padrão para o solo estudado, com valores maiores em profundidade do que na camada mais superficial. Houve maior estabilidade temporal da armazenagem de água no solo durante o período chuvoso, porém na fase de secagem do solo a estabilidade temporal também foi constatada, mas com valores de coeficiente de correlação mais elevados na camada de 0,0-0,80 m, mostrando que essa estabilidade foi claramente devida à posição topográfica desses pontos, os quais estão localizados na porção mais baixa do relevo. Assim, o ponto 52 foi escolhido como representativo da média na fase de recarga de água no solo em ambas as camadas estudadas, e o ponto 46, na camada superior durante a fase de secagem do solo. A dependência espacial da variabilidade da armazenagem de água no solo foi detectada em ambas as camadas de solo, porém com maior alcance na camada de 0,0-0,40 m, quando houve ocorrência de precipitação. Quando as chuvas cessaram, o alcance foi maior na camada de 0,0-0,80 m. Durante o período chuvoso, o padrão de variabilidade espacial foi muito semelhante em ambas as camadas de solo, com armazenagens maiores na faixa de maior inclinação e depressões do terreno.

Spatio-temporal variability of sugarcane yield efficiency in the state of São Paulo, Brazil

The objective of this work was to assess the spatial and temporal variability of sugarcane yield efficiency and yield gap in the state of São Paulo, Brazil, throughout 16 growing seasons, considering climate and soil as main effects, and socioeconomic factors as complementary. An empirical model was used to assess potential and attainable yields, using climate data series from 37 weather stations. Soil effects were analyzed using the concept of production environments associated with a soil aptitude map for sugarcane. Crop yield efficiency increased from 0.42 to 0.58 in the analyzed period (1990/1991 to 2005/2006 crop seasons), and yield gap consequently decreased from 58 to 42%. Climatic factors explained 43% of the variability of sugarcane yield efficiency, in the following order of importance: solar radiation, water deficit, maximum air temperature, precipitation, and minimum air temperature. Soil explained 15% of the variability, considering the average of all seasons. There was a change in the correlation pattern of climate and soil with yield efficiency after the 2001/2002 season, probably due to the crop expansion to the west of the state during the subsequent period. Socioeconomic, biotic and crop management factors together explain 42% of sugarcane yield efficiency in the state of São Paulo.

Space-temporal dynamics of limnological variables in a floodplain wetland located at Ribeira do Iguape Valley (São Paulo, Brazil) at different hydrological periods

AIM: The main goal of this research was to investigate the influence of the hydrological pulses on the space-temporal dynamics of physical and chemical variables in a wetland adjacent to Jacupiranguinha River (São Paulo, Brazil); METHODS: Eleven sampling points were distributed among the wetland, a tributary by its left side and the adjacent river. Four samplings were carried out, covering the rainy and the dry periods. Measures of pH, dissolved oxygen, electrical conductivity and redox potential were taken in regular intervals of the water column using a multiparametric probe. Water samples were collected for the nitrogen and total phosphorus analysis, as well as their dissolved fractions (dissolved inorganic phosphorus, total dissolved phosphorus, ammoniacal nitrogen and nitrate). Total alkalinity and suspended solids were also quantified; RESULTS: The Multivariate Analysis of Variance showed the influence of the seasonality on the variability of the investigated variables, while the Principal Component Analysis gave rise in two statistical significant axes, which delimited two groups representative of the rainy and dry periods. Hydrological pulses from Jacupiranguinha River, besides contributing to the inputs of nutrients and sediments during the period of connectivity, accounted for the decrease in spatial gradients in the wetland. This "homogenization effect" was evidenced by the Cluster Analysis. The research also showed an industrial raw effluent as the main point source of phosphorus to the Jacupiranguinha River and, indirectly, to the wetland; CONCLUSIONS: Therefore, considering the scarcity of information about the wetlands in the study area, this research, besides contributing to the understanding of the influence of hydrological pulses on the investigated environmental variables, showed the need for adoption of conservation policies of these ecosystems face the increase anthropic pressures that they have been submitted, which may result in lack of their ecological, social and economic functions.

Temporal and along-shelf distribution of the larval fish assemblage at Gran Canaria, Canary Islands

Temporal and spatial variations of the larval fish community off the island of Gran Canaria (Canary Islands) were studied in weekly surveys from October 2005 to June 2006. A total of 156 taxa, belonging to 51 families and 15 orders, were identified. Myctophidae was by far the most abundant family (30%), followed by Sparidae (11%), Clupeidae (9%) and Gonostomatidae (7%). As expected for an oceanic island, neritic and oceanic taxa contributed in similar proportions. Leeward and windward retention areas were found for total egg and neritic larval abundance. However, seasonality showed a stronger influence on the annual larval assemblage than sampling site, as the latter was not significant on a long time scale. Results suggest that there are two seasonal larval assemblages corresponding to the two main characteristic periods of the water column in these waters: mixing (winter) and stratification (summer). In addition, a significant relationship was recorded between lunar illumination and small mesozooplankton biomass, suggesting that this relationship may be extended to certain neritic families. The most abundant neritic larvae (Sparidae) showed this lunar pattern, which partially supports a recent hypothesis about the effect of lunar illumination on larval fish survival and development in subtropical waters.

Análisis espacio-temporal de las praderas de Cymodocea nodosa (Ucria) Ascherson en la isla de Gran Canaria

Máster Oficial en Gestión Costera

Optical flow estimation with consistent spatio-temporal coherence models

[EN] In this work we propose a new variational model for the consistent estimation of motion fields. The aim of this work is to develop appropriate spatio-temporal coherence models. In this sense, we propose two main contributions: a nonlinear flow constancy assumption, similar in spirit to the nonlinear brightness constancy assumption, which conveniently relates flow fields at different time instants; and a nonlinear temporal regularization scheme, which complements the spatial regularization and can cope with piecewise continuous motion fields. These contributions pose a congruent variational model since all the energy terms, except the spatial regularization, are based on nonlinear warpings of the flow field. This model is more general than its spatial counterpart, provides more accurate solutions and preserves the continuity of optical flows in time. In the experimental results, we show that the method attains better results and, in particular, it considerably improves the accuracy in the presence of large displacements.

Variabilidad espacio-temporal de la biomasa de la capa profunda de reflexión en aguas canarias

[ES] La Capa Profunda de Reflexión (Deep Scattering Layer, DSL) es una capa de reflexión bioacústica formada por organismos mesopelágicos y constituye uno de los recursos biológicos marinos más abundantes de las Aguas de Canarias. Utilizando los datos obtenidos mediante técnicas acústicas y de arrastres pelágicos realizados en estas aguas durante diferentes campañas, investigamos la distribución espacio-temporal de la biomasa de las comunidades mesopelágicas que la componen.

Bioimaging of animal embryogenesis: mathematical methods and computational algorithms

Some fundamental biological processes such as embryonic development have been preserved during evolution and are common to species belonging to different phylogenetic positions, but are nowadays largely unknown. The understanding of cell morphodynamics leading to the formation of organized spatial distribution of cells such as tissues and organs can be achieved through the reconstruction of cells shape and position during the development of a live animal embryo. We design in this work a chain of image processing methods to automatically segment and track cells nuclei and membranes during the development of a zebrafish embryo, which has been largely validates as model organism to understand vertebrate development, gene function and healingrepair mechanisms in vertebrates. The embryo is previously labeled through the ubiquitous expression of fluorescent proteins addressed to cells nuclei and membranes, and temporal sequences of volumetric images are acquired with laser scanning microscopy. Cells position is detected by processing nuclei images either through the generalized form of the Hough transform or identifying nuclei position with local maxima after a smoothing preprocessing step. Membranes and nuclei shapes are reconstructed by using PDEs based variational techniques such as the Subjective Surfaces and the Chan Vese method. Cells tracking is performed by combining informations previously detected on cells shape and position with biological regularization constraints. Our results are manually validated and reconstruct the formation of zebrafish brain at 7-8 somite stage with all the cells tracked starting from late sphere stage with less than 2% error for at least 6 hours. Our reconstruction opens the way to a systematic investigation of cellular behaviors, of clonal origin and clonal complexity of brain organs, as well as the contribution of cell proliferation modes and cell movements to the formation of local patterns and morphogenetic fields.

Spatio-temporal variation of macrofaunal assemblages in the deep Blanes submarine canyon

The spatio-temporal variations in diversity and abundance of deep-sea macrofaunal assemblages (excluding meiofaunal taxa, as Nematoda, Copepoda and Ostracoda) from the Blanes Canyon (BC) and adjacent open slope are described. The Catalan Sea basin is characterized by the presence of numerous submarine canyons, which are globally acknowledged as biodiversity hot-spots, due to their disturbance regime and incremented conveying of organic matter. This area is subjected to local deep-sea fisheries activities, and to recurrent cold water cascading events from the shelf. The upper canyon (~900 m), middle slope (~1200 m) and lower slope (~1500 m) habitats were investigated during three different months (October 2008, May 2009 and September 2009). A total of 624 specimens belonging to 16 different taxa were found into 67 analyzed samples, which had been collected from the two study areas. Of these, Polychaeta, Mollusca and Crustacea were always the most abundant groups. As expected, the patterns of species diversity and evenness were different in time and space. Both in BC and open slope, taxa diversity and abundance are higher in the shallowest depth and lowest at -1500 m depth. This is probably due to different trophic regimes at these depths. The abundance of filter-feeders is higher inside BC than in the adjacent open slope, which is also related with an increment of predator polychaetes. Surface deposit-feeders are more abundant in the open slope than in BC, along with a decrement of filter-feeders and their predators. Probably these differences are due to higher quantities of suspended organic matter reaching the canyon. The multivariate analyses conducted on major taxa point out major differences effective taxa richness between depths and stations. In September 2009 the analyzed communities double their abundances, with a corresponding increase in richness of taxa. This could be related to a mobilizing event, like the release of accumulated food-supply in a nepheloid layer associated to the arrival of autumn. The highest abundance in BC is detected in the shallowest depth and in late summer (September), probably due to higher food availability caused by stronger flood events coming from Tordera River. The effects of such events seemed to involve adjacent open slope too. The nMDS conducted on major taxa abundance shows a slight temporal difference between the three campaigns samples, with a clear clustering between samples of Sept 09. All depth and all months were dominated by Polychaeta, which have been identified to family level and submitted to further analysis. Family richness have clearly minimum at the -1200 m depth of BC, highlighting the presence of a general impact affecting the populations in the middle slope. Three different matrices have been created, each with a different taxonomic level (All Taxa “AT”, Phylum Level “PL” and Polychaeta Families “PF”). Multivariate analysis (MDS, SIMPER) conducted on PL matrix showed a clear spatial differences between stations (BC and open slope) and depths. MDSs conducted on other two matrices (AT and PF) showed similar patterns, but different from PL analysis. A 2 nd stage analysis have been conducted to understand differences between different taxonomic levels, and PL level has been chosen as the most representative of variation. The faunal differences observed were explained by depth, station and season. All work has been accomplished in the Centre d’estudis avançats de Blanes (CEAB-CSIC), within the framework of Spanish PROMETEO project "Estudio Integrado de Cañones y Taludes PROfundos del MEdiTErráneo Occidental: un hábitat esencial", Ref. CTM2007-66316-C02- 01/MAR.

Sea Level Variations from Decades to Millennia: A few Case Studies

The main goals of this Ph.D. study are to investigate the regional and global geophysical components related to present polar ice melting and to provide independent cross validation checks of GIA models using both geophysical data detected by satellite mission, and geological observations from far field sites, in order to determine a lower and upper bound of uncertainty of GIA effect. The subject of this Thesis is the sea level change from decades to millennia scale. Within ice2sea collaboration, we developed a Fortran numerical code to analyze the local short-term sea level change and vertical deformation resulting from the loss of ice mass. This method is used to investigate polar regions: Greenland and Antarctica. We have used mass balance based on ICESat data for Greenland ice sheet and a plausible mass balance for Antarctic ice sheet. We have determined the regional and global fingerprint of sea level variations, vertical deformations of the solid surface of the Earth and variations of shape of the geoid for each ice source mentioned above. The coastal areas are affected by the long wavelength component of GIA process. Hence understanding the response of the Earth to loading is crucial in various contexts. Based on the hypothesis that Earth mantle materials obey to a linear rheology, and that the physical parameters of this rheology can be only characterized by their depth dependence, we investigate the Glacial Isostatic Effect upon the far field sites of Mediterranean area using an improved SELEN program. We presented new and revised observations for archaeological fish tanks located along the Tyrrhenian and Adriatic coast of Italy and new RSL for the SE Tunisia. Spatial and temporal variations of the Holocene sea levels studied in central Italy and Tunisia, provided important constraints on the melting history of the major ice sheets.

The spatial representation of time

Numerosi studi mostrano che gli intervalli temporali sono rappresentati attraverso un codice spaziale che si estende da sinistra verso destra, dove gli intervalli brevi sono rappresentati a sinistra rispetto a quelli lunghi. Inoltre tale disposizione spaziale del tempo può essere influenzata dalla manipolazione dell’attenzione-spaziale. La presente tesi si inserisce nel dibattito attuale sulla relazione tra rappresentazione spaziale del tempo e attenzione-spaziale attraverso l’uso di una tecnica che modula l’attenzione-spaziale, ovvero, l’Adattamento Prismatico (AP). La prima parte è dedicata ai meccanismi sottostanti tale relazione. Abbiamo mostrato che spostando l’attenzione-spaziale con AP, verso un lato dello spazio, si ottiene una distorsione della rappresentazione di intervalli temporali, in accordo con il lato dello spostamento attenzionale. Questo avviene sia con stimoli visivi, sia con stimoli uditivi, nonostante la modalità uditiva non sia direttamente coinvolta nella procedura visuo-motoria di AP. Questo risultato ci ha suggerito che il codice spaziale utilizzato per rappresentare il tempo, è un meccanismo centrale che viene influenzato ad alti livelli della cognizione spaziale. La tesi prosegue con l’indagine delle aree corticali che mediano l’interazione spazio-tempo, attraverso metodi neuropsicologici, neurofisiologici e di neuroimmagine. In particolare abbiamo evidenziato che, le aree localizzate nell’emisfero destro, sono cruciali per l’elaborazione del tempo, mentre le aree localizzate nell’emisfero sinistro sono cruciali ai fini della procedura di AP e affinché AP abbia effetto sugli intervalli temporali. Infine, la tesi, è dedicata allo studio dei disturbi della rappresentazione spaziale del tempo. I risultati ci indicano che un deficit di attenzione-spaziale, dopo danno emisferico destro, provoca un deficit di rappresentazione spaziale del tempo, che si riflette negativamente sulla vita quotidiana dei pazienti. Particolarmente interessanti sono i risultati ottenuti mediante AP. Un trattamento con AP, efficace nel ridurre il deficit di attenzione-spaziale, riduce anche il deficit di rappresentazione spaziale del tempo, migliorando la qualità di vita dei pazienti.

Methods for Clearance Influence Analysis in Planar and Spatial Mechanisms

This doctoral dissertation presents a new method to asses the influence of clearancein the kinematic pairs on the configuration of planar and spatial mechanisms. The subject has been widely investigated in both past and present scientific literature, and is approached in different ways: a static/kinetostatic way, which looks for the clearance take-up due to the external loads on the mechanism; a probabilistic way, which expresses clearance-due displacements using probability density functions; a dynamic way, which evaluates dynamic effects like the actual forces in the pairs caused by impacts, or the consequent vibrations. This dissertation presents a new method to approach the problem of clearance. The problem is studied from a purely kinematic perspective. With reference to a given mechanism configuration, the pose (position and orientation) error of the mechanism link of interest is expressed as a vector function of the degrees of freedom introduced in each pair by clearance: the presence of clearance in a kinematic pair, in facts, causes the actual pair to have more degrees of freedom than the theoretical clearance-free one. The clearance-due degrees of freedom are bounded by the pair geometry. A proper modelling of clearance-affected pairs allows expressing such bounding through analytical functions. It is then possible to study the problem as a maximization problem, where a continuous function (the pose error of the link of interest) subject to some constraints (the analytical functions bounding clearance- due degrees of freedom) has to be maximize. Revolute, prismatic, cylindrical, and spherical clearance-affected pairs have been analytically modelled; with reference to mechanisms involving such pairs, the solution to the maximization problem has been obtained in a closed form.

Modeling the spatial dynamics of economic models

The advances that have been characterizing spatial econometrics in recent years are mostly theoretical and have not found an extensive empirical application yet. In this work we aim at supplying a review of the main tools of spatial econometrics and to show an empirical application for one of the most recently introduced estimators. Despite the numerous alternatives that the econometric theory provides for the treatment of spatial (and spatiotemporal) data, empirical analyses are still limited by the lack of availability of the correspondent routines in statistical and econometric software. Spatiotemporal modeling represents one of the most recent developments in spatial econometric theory and the finite sample properties of the estimators that have been proposed are currently being tested in the literature. We provide a comparison between some estimators (a quasi-maximum likelihood, QML, estimator and some GMM-type estimators) for a fixed effects dynamic panel data model under certain conditions, by means of a Monte Carlo simulation analysis. We focus on different settings, which are characterized either by fully stable or quasi-unit root series. We also investigate the extent of the bias that is caused by a non-spatial estimation of a model when the data are characterized by different degrees of spatial dependence. Finally, we provide an empirical application of a QML estimator for a time-space dynamic model which includes a temporal, a spatial and a spatiotemporal lag of the dependent variable. This is done by choosing a relevant and prolific field of analysis, in which spatial econometrics has only found limited space so far, in order to explore the value-added of considering the spatial dimension of the data. In particular, we study the determinants of cropland value in Midwestern U.S.A. in the years 1971-2009, by taking the present value model (PVM) as the theoretical framework of analysis.