Advanced geostatistical and machine-learning models for spatial data analysis of radioactively contaminated regions

Radioactive soil-contamination mapping and risk assessment is a vital issue for decision makers. Traditional approaches for mapping the spatial concentration of radionuclides employ various regression-based models, which usually provide a single-value prediction realization accompanied (in some cases) by estimation error. Such approaches do not provide the capability for rigorous uncertainty quantification or probabilistic mapping. Machine learning is a recent and fast-developing approach based on learning patterns and information from data. Artificial neural networks for prediction mapping have been especially powerful in combination with spatial statistics. A data-driven approach provides the opportunity to integrate additional relevant information about spatial phenomena into a prediction model for more accurate spatial estimates and associated uncertainty. Machine-learning algorithms can also be used for a wider spectrum of problems than before: classification, probability density estimation, and so forth. Stochastic simulations are used to model spatial variability and uncertainty. Unlike regression models, they provide multiple realizations of a particular spatial pattern that allow uncertainty and risk quantification. This paper reviews the most recent methods of spatial data analysis, prediction, and risk mapping, based on machine learning and stochastic simulations in comparison with more traditional regression models. The radioactive fallout from the Chernobyl Nuclear Power Plant accident is used to illustrate the application of the models for prediction and classification problems. This fallout is a unique case study that provides the challenging task of analyzing huge amounts of data ('hard' direct measurements, as well as supplementary information and expert estimates) and solving particular decision-oriented problems.

A comparison of rapid bioassessment protocols used in 2 regions with Mediterranean climates, the Iberian Peninsula and South Africa

Abstract. The ability of 2 Rapid Bioassessment Protocols (RBPs) to assess stream water quality was compared in 2 Mediterranean-climate regions. The most commonly used RBPs in South Africa (SAprotocol) and the Iberian Peninsula (IB-protocol) are both multihabitat, field-based methods that use macroinvertebrates. Both methods use preassigned sensitivity weightings to calculate metrics and biotic indices. The SA- and IB-protocols differ with respect to sampling equipment (mesh size: 1000 lm vs 250 300 lm, respectively), segregation of habitats (substrate vs flow-type), and sampling and sorting procedures (variable time and intensity). Sampling was undertaken at 6 sites in South Africa and 5 sites in the Iberian Peninsula. Forty-four and 51 macroinvertebrate families were recorded in South Africa and the Iberian Peninsula, respectively; 77.3% of South African families and 74.5% of Iberian Peninsula families were found using both protocols. Estimates of community similarity compared between the 2 protocols were .60% similar among sites in South Africa and .54% similar among sites in the Iberian Peninsula (BrayCurtis similarity), and no significant differences were found between protocols (Multiresponse Permutation Procedure). Ordination based on Non-metric Multidimensional Scaling grouped macroinvertebrate samples on the basis of site rather than protocol. Biotic indices generated with the 2 protocols at each site did not differ. Thus, both RBPs produced equivalent results, and both were able to distinguish between biotic communities (mountain streams vs foothills) and detect water-quality impairment, regardless of differences in sampling equipment, segregation of habitats, and sampling and sorting procedures. Our results indicate that sampling a single habitat may be sufficient for assessing water quality, but a multihabitat approach to sampling is recommended where intrinsic variability of macroinvertebrate assemblages is high (e.g., in undisturbed sites in regions with Mediterranean climates). The RBP of choice should depend on whether the objective is routine biomonitoring of water quality or autecological or faunistic studies.

One-year prevalence of low back pain in two Swiss regions: estimates from the population participating in the 1992-1993 MONICA project.

STUDY DESIGN: A cross-sectional survey was performed. OBJECTIVE: To estimate the extent of low back pain as a public health problem. SUMMARY OF BACKGROUND DATA: Health surveys converge on very high estimates of low back pain in general populations, but few studies have included severity criteria in their definition and conclusions. Because it is unlikely that interventions will influence the prevalence of minimal and infrequent symptoms, greater attention should be paid to characteristics of low back pain that indicate some impact on the life of survey respondents. METHODS: Two regions participated in the MONICA (MONitoring of trends and determinants in CArdiovascular disease) project in Switzerland. Participants randomly selected from the general population completed a standard self-administered questionnaire on cardiovascular risk factors. A special section on low back pain was added in the third (1992-1993) MONICA survey and completed by 3227 participants. RESULTS: A regional difference found in the 12-month prevalence rate disappeared with the inclusion of severity criteria. Low back pain over more than seven cumulated days was reported among men by 20.2% (age range, 25-34 years) to 28.5% (age range, 65-74 years), respectively, among women by 31.1% to 38.5%. Similar rates of reduction in activity (professional, housekeeping, and leisure time) and medical consultation (conventional and nonconventional) motivated by low back pain characterized the two participating regions. The cumulative duration of pain was related to all the indicators showing the impact of low back pain on everyday life. CONCLUSIONS: Determining the cumulative duration of low back pain over the preceding year is a straightforward task, and a cutoff at 1 week seems appropriate for distinguishing between low- and high-impact low back pain.

A Small World Perspective on Urban Systems

The theory of small-world networks as initiated by Watts and Strogatz (1998) has drawn new insights in spatial analysis as well as systems theory. The theoryâeuro?s concepts and methods are particularly relevant to geography, where spatial interaction is mainstream and where interactions can be described and studied using large numbers of exchanges or similarity matrices. Networks are organized through direct links or by indirect paths, inducing topological proximities that simultaneously involve spatial, social, cultural or organizational dimensions. Network synergies build over similarities and are fed by complementarities between or inside cities, with the two effects potentially amplifying each other according to the âeurooepreferential attachmentâeuro hypothesis that has been explored in a number of different scientific fields (Barabási, Albert 1999; Barabási A-L 2002; Newman M, Watts D, Barabàsi A-L). In fact, according to Barabási and Albert (1999), the high level of hierarchy observed in âeurooescale-free networksâeuro results from âeurooepreferential attachmentâeuro, which characterizes the development of networks: new connections appear preferentially close to nodes that already have the largest number of connections because in this way, the improvement in the network accessibility of the new connection will likely be greater. However, at the same time, network regions gathering dense and numerous weak links (Granovetter, 1985) or network entities acting as bridges between several components (Burt 2005) offer a higher capacity for urban communities to benefit from opportunities and create future synergies. Several methodologies have been suggested to identify such denser and more coherent regions (also called communities or clusters) in terms of links (Watts, Strogatz 1998; Watts 1999; Barabási, Albert 1999; Barabási 2002; Auber 2003; Newman 2006). These communities not only possess a high level of dependency among their member entities but also show a low level of âeurooevulnerabilityâeuro, allowing for numerous redundancies (Burt 2000; Burt 2005). The SPANGEO project 2005âeuro"2008 (SPAtial Networks in GEOgraphy), gathering a team of geographers and computer scientists, has included empirical studies to survey concepts and measures developed in other related fields, such as physics, sociology and communication science. The relevancy and potential interpretation of weighted or non-weighted measures on edges and nodes were examined and analyzed at different scales (intra-urban, inter-urban or both). New classification and clustering schemes based on the relative local density of subgraphs were developed. The present article describes how these notions and methods contribute on a conceptual level, in terms of measures, delineations, explanatory analyses and visualization of geographical phenomena.

Effects of genetics and environment on isoflavone content of soybean from different regions of Brazil

The effects of genetics and environmental factors on isoflavone content of soybean (Glycine max L.) cultivars grown in different locations in Brazil in 1993/94 were evaluated. Seeds of different cultivars were analised by high performance liquid chromatography (HPLC). In Rio Grande do Sul (RS), Paraná (PR), and Mato Grosso do Sul (MS) States, a significant difference in the isoflavone total content average of the cultivars IAS 5 and FT-Abyara (163.9, 116.4 and 79.5 mg/100 g, respectively) was observed. In general, IAS 5 contained higher isoflavone than FT-Abyara. Cultivars IAS 5 and FT-Abyara grown at Vacaria, RS (28°30' S latitude) with temperature average of 19°C, had the highest isoflavone concentrations (218.7 and 163.8 mg/100 g, respectively). In Palotina, PR (24°27' S latitude), where temperature average was 24°C, the isoflavone concentrations were 105.9 and 86.8 mg/100 g, respectively. The lowest isoflavone contents were observed for FT-Estrela and FT-Cristalina, (27.6 and 46.5 mg/100 g, repectively) at Rondonópolis, MT (16°20' S latitude), where the temperature was 27°C.

Segmentation of Head and Neck Lymph Node Regions for Radiotherapy Planning Using Active Contour-Based Atlas Registration

In this paper, we present the segmentation of the headand neck lymph node regions using a new active contourbased atlas registration model. We propose to segment thelymph node regions without directly including them in theatlas registration process; instead, they are segmentedusing the dense deformation field computed from theregistration of the atlas structures with distinctboundaries. This approach results in robust and accuratesegmentation of the lymph node regions even in thepresence of significant anatomical variations between theatlas-image and the patient's image to be segmented. Wealso present a quantitative evaluation of lymph noderegions segmentation using various statistical as well asgeometrical metrics: sensitivity, specificity, dicesimilarity coefficient and Hausdorff distance. Acomparison of the proposed method with two other state ofthe art methods is presented. The robustness of theproposed method to the atlas selection, in segmenting thelymph node regions, is also evaluated.

Stable O and H isotopic composition of hydrous minerals as proxies for paleoclimate and -topography : application to the European Alps

The isotopie composition of clay minerals can be used to gain information on paleoaltitude, -topography and -climate during the time of their formation, as they form in isotopie equilibrium with ambient water, which has an isotopie composition that is determined by previous rain-out. In this thesis, the usability of this approach is evaluated for sample material from both the North Alpine Foreland Basin and internal parts of the European Alps. The isotopie composition of precipitation is determined by the air temperature and the extent of previous rain-out, which in turn is affected by the distance to the point of origin of the water vapor and the condensation conditions. An orographic barrier leads to uplift and adiabatic cooling of air masses and thereby enhances rainfall with a characteristic depletion in heavy 0 and H isotopes. Processes such as evaporation and mixing of water with different origin affect the isotopie composition further on the surface. Clay minerals are hydrous phyllosilicates that can form during weathering or pedogenesis in isotopie equilibrium with the present water and inherit its isotopie composition with a characteristic fractionation. If their isotopie composition was preserved after formation and the necessary parameters are known, it is possible to calculate the isotopie composition of the ambient water and thereby reconstruct climatic and topographic conditions during their formation. Due to the hygroscopic behavior of the sample material, analytical procedures needed to be modified to allow an analysis of the oxygen and hydrogen isotopie composition of the hydroxyl water built into their crystal structure and not the one of recently adsorbed water. In order to determine typical 5lsO and 8D values of meteoric water and minerals in the weathering environment in high Alpine regions, samples of surface water and soils from the valley of Visp in the Swiss Alps were studied that were collected along a transect with varying altitudes and host rock lithologies. The actual aim to attempt the reconstruction of Alpine paleoelevations was addressed by the analysis of sediments deposited under marine and terrestrial conditions during the Miocene and Oligocene, which were sampled from different locations in Switzerland, Germany and Austria. Further bentonite and fault gouge clay samples were used as reference material from low and high elevations. Results show that the isotopie composition of clay minerals can be influenced by several factors, such as the mode and site of their formation, possible isotope exchange (which is evident for 8D values), the samples' mineral composition (such as the presence of detrital material) and the deposition environment. With a consideration of these parameters and limitation to certain sample material, conclusions are drawn on the isotopie composition of the water from which the clay minerals formed. Most of the obtained values lie in the same range as has been reported in literature for foreland precipitation. The reconstruction of paleoelevation might be possible for selected sites with a geographical setting close to the Alpine chain or for intramontane basins. - La composition isotopique des argiles, qui se forment typiquement en contact avec des eaux superficielles, peut être utilisée pour obtenir des informations sur la paléoaltitude, la paléotopographie et le paléoclimat pendant leur création. La composition en isotopes stable (oxygène et hydrogène) des eaux de pluie est déterminée par l'altitude, la température, la distance depuis le lieu d'évaporation et par le taux de précipitation. Certains processus comme l'évaporation, l'interaction avec des minéraux et le mélange d'eaux d'origines variées peuvent aussi changer la composition des eaux de surface. Les argiles sont des pliyllosilicates hydratés qui sont crées par l'altération des roches au contact de ces eaux de surface et ils acquièrent une composition isotopique qui est soumise à un certain fractionnement. L'objectif de cette thèse est d'évaluer si l'effet de l'altitude des Alpes, est détectable dans la composition isotopique des sédiments du bassin d'avant-pavs pendant le Miocène. Après avoir établi la procédure analytique, des compositions isotopiques typiques de régions de hautes altitudes ont été determine sur les eaux de surfaces (rivières) et sur des échantillons de sols, le long d'une coupe dans la valée de Visp, dans les Alpes Suisses. Une reconstruction des paléoaltitudes Miocènes Alpines a ensuite été mené par l'analyse de sédiments marins et terrestres en utilisant des échantillons d'âges variés et provenant de Suisse, d'Allemagne et d'Autriche. Les résultats montrent que la composition isotopique des échantillons est impactée par de multiples facteurs, tels que le mode de et le lieu de formation. un possible échange isotopique tardif (surtout pour 5D). leur composition minéralogique et l'environnement de leur sédimentation. Après un examen prudent de ces paramètres, et en se limitant à un certain assortiment d'échatillons, on peut tirer des conclusions sur la composition isotopique des eaux originelles pour en déduire l'effet du climat et de la topographie.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

Influence of row spacing reduction on maize grain yield in regions with a short summer

The interest in reducing maize row spacing in the short growing season regions of Brazil is increasing due to potential advantages such as higher radiation use efficiency. This experiment was conducted to evaluate the effect of row spacing reduction on grain yield of different maize cultivars planted at different dates. The trial was conducted in Lages, in the State of Santa Catarina, Brazil, during 1996/97 and 1997/98 growing seasons, in a split-split plot design. Early (October 1st) and normal (November 15) planting dates were tested in the main plot; two morphologically contrasting cultivars (an early single-cross and a late double-cross hybrids) were evaluated in the split plots and three row widths (100, 75 and 50 cm) were studied in the split-split plots. The reduction of row spacing from 100 to 50 cm increased linearly maize grain yield. The yield edge provided by narrow rows was higher when maize was sown earlier in the season. Differences in hybrid cycle and plant architecture did not alter maize response to the reduction of row spacing.

Tagging reveals limited exchange of immature loggerhead sea turtles (Caretta caretta) between regions in the western Mediterranean.

Exchange of immature loggerhead sea turtles (Caretta caretta) between the northern and southern regions of the western Mediterranean was investigated using data obtained from several Spanish tagging programmes. Tagged turtles ranged in straight carapace length from 23.0 to 74.0 cm. Thirty-six turtles were recaptured after an average interval of 390.5±462.6 days (SD). As the mean dispersal distance (MDD) of a turtle population that spreads over the western Mediterranean would stabilize after 117 days (CI 95%: 98 to 149), two analyses were conducted that included data from turtles recaptured after 98 and 149 days respectively. In both analyses, turtles were recaptured more often than expected in the same region where they had been tagged. No difference was found in either of the two regions between the average distance between the capture and recapture locations and the expected MDD if the turtles were to remain in the region where they were first captured. Turtles recaptured after 15 and 25 days respectively were excluded from the analysis to ensure data independence. The overall evidence indicates that immature turtles exhibit strong site fidelity to certain areas and that there is a strong barrier to dispersal between the northern and southern parts of the western Mediterranean. Therefore, loggerhead turtles in the western Mediterranean should be split into at least two management units.

Dissecting the role of low-complexity regions in the evolution of vertebrate proteins

Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few aminoacids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution. We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance. We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.

Variation in the proportion of flower visitors of Arum maculatum along its distributional range in relation with community‐based climatic niche analyses

Here, we investigate the geographical constancy in the specificity level of the specialized lure-and-trap pollination antagonism involving the widespread European Arum maculatum and its associated Psychodid pollinators. Until now, studies concurred in demonstrating that one single insect species, Psychoda phalaenoides, efficiently cross-pollinated plants; researches were, however, performed locally in western Europe. In this study we characterize for the first time the flower visitors' composition at the scale of the distribution range of A. maculatum by intensively collecting plants and insects throughout the European continent. We further correlate local climatic characteristics with the community composition of visiting arthropods.Our results show that flowers are generally visited by P. phalaenoides females, but not over the whole distribution range of the plant. In some regions this fly species is less frequent or even absent and another species, Psycha grisescens, becomes the prevailing visitor. This variability is geographically structured and can be explained by climatic factors: the proportion of P. grisescens increases with higher annual precipitations and lower precipitations in the warmest trimester, two characteristics typical of the Mediterranean zone. Climate thus seems driving the specificity of this interaction, by potentially affecting the phenology of one or both interacting species, or even of volatile and heat production in the plant. This result therefore challenges the specificity of other presumably one-to-one interactions covering wide distribution ranges, and provides an example of the direct effect that the abiotic environment can have on the fate of plant-insect interactions.

Regional income inequality in Italy in the long run (1871–2001). Patterns and determinants

The chapter presents up-to-date estimates of Italy’s regional GDP, with the present borders, in ten-year benchmarks from 1871 to 2001, and proposes a new interpretative hypothesis based on long-lasting socio-institutional differences. The inverted U-shape of income inequality is confirmed: rising divergence until the midtwentieth century, then convergence. However, the latter was limited to the centrenorth: Italy was divided into three parts by the time regional inequality peaked, in 1951, and appears to have been split into two halves by 2001. As a consequence of the falling back of the south, from 1871 to 2001 we record σ-divergence across Italy’s regions, i.e. an increase in dispersion, and sluggish β-convergence. Geographical factors and the market size played a minor role: against them are both the evidence that most of the differences in GDP are due to employment rather than to productivity and the observed GDP patterns of many regions. The gradual converging of regional GDPs towards two equilibria instead follows social and institutional differences − in the political and economic institutions and in the levels of human and social capital – which originated in pre-unification states and did not die (but in part even increased) in postunification Italy.