Exploring the interplay between natural decadal variability and anthropogenic climate change in summer rainfall over China. Part I: Observational evidence

Summer rainfall over China has experienced substantial variability on longer time scales during the last century, and the question remains whether this is due to natural, internal variability or is part of the emerging signal of anthropogenic climate change. Using the best available observations over China, the decadal variability and recent trends in summer rainfall are investigated with the emphasis on changes in the seasonal evolution and on the temporal characteristics of daily rainfall. The possible relationships with global warming are reassessed. Substantial decadal variability in summer rainfall has been confirmed during the period 1958–2008; this is not unique to this period but is also seen in the earlier decades of the twentieth century. Two dominant patterns of decadal variability have been identified that contribute substantially to the recent trend of southern flooding and northern drought. Natural decadal variability appears to dominate in general but in the cases of rainfall intensity and the frequency of rainfall days, particularly light rain days, then the dominant EOFs have a rather different character, being of one sign over most of China, and having principal components (PCs) that appear more trendlike. The increasing intensity of rainfall throughout China and the decrease in light rainfall days, particularly in the north, could at least partially be of anthropogenic origin, both global and regional, linked to increased greenhouse gases and increased aerosols.

Promoting the use of BaP as a marker for PAH exposure in UK soils

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants that frequently accumulate in soils. There is therefore a requirement to determine their levels in contaminated environments for the purposes of determining impacts on human health. PAHs are a suite of individual chemicals, and there is an ongoing debate as to the most appropriate method for assessing the risk to humans from them. Two methods predominate: the surrogate marker approach and the toxic equivalency factor. The former assumes that all chemicals in a mixture have an equivalent toxicity. The toxic equivalency approach estimates the potency of individual chemicals relative to the usually most toxic Benzo(a)pyrene. The surrogate marker approach is believed to overestimate risk and the toxic equivalency factor to underestimate risk. When analysing the risks from soils, the surrogate marker approach is preferred due to its simplicity, but there are concerns because of the potential diversity of the PAH profile across the range of impacted soils. Using two independent data sets containing soils from 274 sites across a diverse range of locations, statistical analysis was undertaken to determine the differences in the composition of carcinogenic PAH between site locations, for example, rural versus industrial. Following principal components analysis, distinct population differences were not seen between site locations in spite of large differences in the total PAH burden between individual sites. Using all data, highly significant correlations were seen between BaP and other carcinogenic PAH with the majority of r2 values > 0.8. Correlations with the European Food Standards Agency (EFSA) summed groups, that is, EFSA2, EFSA4 and EFSA8 had even higher correlations (r2 > 0.95). We therefore conclude that BaP is a suitable surrogate marker to represent mixtures of PAH in soil during risk assessments.

Geochemical changes recorded in Lynch's Crater, Northeastern Australia, over the past 50 ka

There are many geochemical reconstructions of environmental change in the mid and high latitudes but relatively few in the tropical latitudes, despite their considerable potential for reconstructing environmental processes that cannot be identified using more traditional proxies. Here we present one reconstruction of environmental change for the tropics. This reconstruction covers the past 50 ka using a suite of geochemical data from the high-resolution sequence of Lynch's Crater in northeast Queensland, Australia, a region highly sensitive to El Niño-Southern Oscillation (ENSO) activity. The 23 major oxides and trace elements measured could be summarised by extracting three axes using principal components analysis (accounting for 72% of the variability). The data indicate that the greatest variability in the geochemical data accounted for erosional activity within the catchment that was associated with past changes in the frequency of ENSO activity (though this was less sensitive during wetter periods, probably as a result of buffering by high vegetation cover). The remaining variability was largely explained by elements that form complexes with organic compounds (e.g., humic acids) and those that are important nutrients for specific vegetation types (and therefore a measure of vegetation distribution). For more detailed reconstructions, further work is required to disentangle the complex controls of elements within sedimentary sequences.

Pollen-based differentiation of Amazonian rainforest communities and implications for lowland palaeoecology in tropical South America

An ongoing controversy in Amazonian palaeoecology is the manner in which Amazonian rainforest communities have responded to environmental change over the last glacial–interglacial cycle. Much of this controversy results from an inability to identify the floristic heterogeneity exhibited by rainforest communities within fossil pollen records. We apply multivariate (Principal Components Analysis) and classification (Unweighted Pair Group with Arithmetic Mean Agglomerative Classification) techniques to floral-biometric, modern pollen trap and lake sediment pollen data situated within different rainforest communities in the tropical lowlands of Amazonian Bolivia. Modern pollen rain analyses from artificial pollen traps show that evergreen terra firme (well-drained), evergreen terra firme liana, evergreen seasonally inundated, and evergreen riparian rainforests may be readily differentiated, floristically and palynologically. Analogue matching techniques, based on Euclidean distance measures, are employed to compare these pollen signatures with surface sediment pollen assemblages from five lakes: Laguna Bella Vista, Laguna Chaplin, and Laguna Huachi situated within the Madeira-Tapajós moist forest ecoregion, and Laguna Isirere and Laguna Loma Suarez, which are situated within forest patches in the Beni savanna ecoregion. The same numerical techniques are used to compare rainforest pollen trap signatures with the fossil pollen record of Laguna Chaplin.

Forecasting by factors, by variables, by both or neither?

We consider forecasting with factors, variables and both, modeling in-sample using Autometrics so all principal components and variables can be included jointly, while tackling multiple breaks by impulse-indicator saturation. A forecast-error taxonomy for factor models highlights the impacts of location shifts on forecast-error biases. Forecasting US GDP over 1-, 4- and 8-step horizons using the dataset from Stock and Watson (2009) updated to 2011:2 shows factor models are more useful for nowcasting or short-term forecasting, but their relative performance declines as the forecast horizon increases. Forecasts for GDP levels highlight the need for robust strategies, such as intercept corrections or differencing, when location shifts occur as in the recent financial crisis.

A metabolic system-wide characterisation of the pig: a model for human physiology

The pig is a single-stomached omnivorous mammal and is an important model of human disease and nutrition. As such, it is necessary to establish a metabolic framework from which pathology-based variation can be compared. Here, a combination of one and two-dimensional 1H and 13C nuclear magnetic resonance spectroscopy (NMR) and high-resolution magic angle spinning (HR-MAS) NMR was used to provide a systems overview of porcine metabolism via characterisation of the urine, serum, liver and kidney metabolomes. The metabolites observed in each of these biological compartments were found to be qualitatively comparable to the metabolic signature of the same biological matrices in humans and rodents. The data were modelled using a combination of principal components analysis and Venn diagram mapping. Urine represented the most metabolically distinct biological compartment studied, with a relatively greater number of NMR detectable metabolites present, many of which are implicated in gut-microbial co-metabolic processes. The major interspecies differences observed were in the phase II conjugation of extra-genomic metabolites; the pig was observed to conjugate p-cresol, a gut microbial metabolite of tyrosine, with glucuronide rather than sulfate as seen in man. These observations are important to note when considering the translatability of experimental data derived from porcine models.

Building the niche through time: using 13,000 years of data to predict the effects of climate change on three tree species in Europe

Aim  Species distribution models (SDMs) based on current species ranges underestimate the potential distribution when projected in time and/or space. A multi-temporal model calibration approach has been suggested as an alternative, and we evaluate this using 13,000 years of data. Location  Europe. Methods  We used fossil-based records of presence for Picea abies, Abies alba and Fagus sylvatica and six climatic variables for the period 13,000 to 1000 yr bp. To measure the contribution of each 1000-year time step to the total niche of each species (the niche measured by pooling all the data), we employed a principal components analysis (PCA) calibrated with data over the entire range of possible climates. Then we projected both the total niche and the partial niches from single time frames into the PCA space, and tested if the partial niches were more similar to the total niche than random. Using an ensemble forecasting approach, we calibrated SDMs for each time frame and for the pooled database. We projected each model to current climate and evaluated the results against current pollen data. We also projected all models into the future. Results  Niche similarity between the partial and the total-SDMs was almost always statistically significant and increased through time. SDMs calibrated from single time frames gave different results when projected to current climate, providing evidence of a change in the species realized niches through time. Moreover, they predicted limited climate suitability when compared with the total-SDMs. The same results were obtained when projected to future climates. Main conclusions  The realized climatic niche of species differed for current and future climates when SDMs were calibrated considering different past climates. Building the niche as an ensemble through time represents a way forward to a better understanding of a species' range and its ecology in a changing climate.

Extensive and intensive globalizations: explicating the low connectivity puzzle of U.S. cities using a city-dyad analysis

This article reports an experiment in world city network analysis focusing on city-dyads. Results are derived from an unusual principal components analysis of 27,966 city-dyads across 5 advanced producer service sectors. A 2-component solution is found that identifies different forms of globalization: extensive and intensive. The latter is characterized by very high component scores and describes the more important city-dyads focused upon London-New York (NYLON). The extensive globalization component heavily features London and New York but with each linked to less important cities. U.S. cities score relatively high on the intensive globalization component and we use this finding to explain the low connectivities of U.S. cities in previous studies of the world city network. The two components are tentatively interpreted in world-systems terms: intensive globalization is the process of core-making through city-dyads; extensive globalization is the process of linking core with non-core through city-dyads.

Reduced-order dynamics of the Martian atmospheric dynamics

In this paper we explore the possibility of deriving low-dimensional models of the dynamics of the Martian atmosphere. The analysis consists of a Proper Orthogonal Decomposition (POD) of the atmospheric streamfunction after first decomposing the vertical structure with a set of eigenmodes. The vertical modes were obtained from the quasi-geostrophic vertical structure equation. The empirical orthogonal functions (EOFs) were optimized to represent the atmospheric total energy. The total energy was used as the criterion to retain those modes with large energy content and discard the rest. The principal components (PCs) were analysed by means of Fourier analysis, so that the dominant frequencies could be identified. It was possible to observe the strong influence of the diurnal cycle and to identify the motion and vacillation of baroclinic waves.

The projected hand illusion: component structure in a community sample, and association with demographics, cognition and psychotic-like experiences

The projected hand illusion (PHI) is a variant of the rubber hand illusion (RHI), and both are commonly used to study mechanisms of self-perception. A questionnaire was developed by Longo et al. (2008) to measure qualitative changes in the RHI. Such psychometric analyses have not yet been conducted on the questionnaire for the PHI. The present study is an attempt to validate minor modifications of the questionnaire of Longo et al. to assess the PHI in a community sample (n = 48) and to determine the association with selected demographic (age, sex, years of education), cognitive (Digit Span), and clinical (psychotic-like experiences) variables. Principal components analysis on the questionnaire data extracted four components: Embodiment of “Other” Hand, Disembodiment of Own Hand, Deafference, and Agency—in both synchronous and asynchronous PHI conditions. Questions assessing “Embodiment” and “Agency” loaded onto orthogonal components. Greater illusion ratings were positively associated with being female, being younger, and having higher scores on psychotic-like experiences. There was no association with cognitive performance. Overall, this study confirmed that self-perception as measured with PHI is a multicomponent construct, similar in many respects to the RHI. The main difference lies in the separation of Embodiment and Agency into separate constructs, and this likely reflects the fact that the “live” image of the PHI presents a more realistic picture of the hand and of the stroking movements of the experimenter compared with the RHI.

Differentiation of neotropical ecosystems by modern soil phytolith assemblages and its implications for palaeoenvironmental and archaeological reconstructions II: Southwestern Amazonian forests

Accurate archaeological and palaeoenvironmental reconstructions using phytoliths relies on the study of modern reference material. In eastern Acre, Brazil, we examined whether the five most common forest types present today were able to be differentiated by their soil phytolith assemblages, and thus provide analogues with which to compare palaeoecological assemblages from pre-Columbian earthwork sites in the region. Surface soils and vegetation from dense humid evergreen forest, dense humid evergreen forest with high palm abundance, palm forest, bamboo forest and fluvial forest were sampled and their phytoliths analysed. Relative phytolith frequencies were statistically compared using Principal Components Analyses (PCAs). We found the major differences in species composition to be well-represented by the phytolith assemblages as all forest types, apart from the two sub-types of dense humid evergreen forest, could be differentiated. Larger phytoliths from the sand fraction were found to be more ecologically diagnostic than those from the silt fraction. The surface soil phytolith assemblages we analysed can therefore be used as analogues to improve the accuracy of archaeological and palaeoecological reconstructions in the region.

Oral health in transition: the case of Indigenous peoples from Brazil

The objective of this paper is to summarise epidemiological information about the distribution of dental caries among Indigenous peoples in Brazil. The authors also present a case study of a specific group of Xavante Indians, one of the most numerous of Brazil`s Indigenous peoples, describing how their oral health has deteriorated over recent decades, and showing how an oral health programme is attempting to reverse the present trend of increase in caries. The programme at Etenheritipa Xavante village incorporated three principal components: educational, preventive, and clinical. From the beginning, the programme included epidemiological record keeping for monitoring the level of caries in the population. Transversal studies of the condition of oral health among the Xavante of Etenheritipa were undertaken in 1999, 2004, and 2007. In the period from 2004 to 2007 the DMFS values in the 11-15 age cohort had a significant reduction in caries experience. The mean DMFS score fell from 4.95 in 2004 to 2.39 in 2007 (p<0.01). An increase in the percent of individuals who were free from caries was also noted: in 1999, 20% of adolescents 11-15 had no caries; in 2007, the proportion had risen to 47%. The Xavante case is a prime example of the transition in oral health that is taking place among the Indigenous peoples of the Americas, and it highlights the importance of oral health promotion through preventive measures such as access to fluoridation and basic care in reducing the inequality between Indians and non-Indians.

Multivariate analysis of the energy cycle of the South American rainy season

The South American (SA) rainy season is studied in this paper through the application of a multivariate Empirical Orthogonal Function (EOF) analysis to a SA gridded precipitation analysis and to the components of Lorenz Energy Cycle (LEC) derived from the National Centers for Environmental Prediction (NCEP) reanalysis. The EOF analysis leads to the identification of patterns of the rainy season and the associated mechanisms in terms of their energetics. The first combined EOF represents the northwest-southeast dipole of the precipitation between South and Central America, the South American Monsoon System (SAMS). The second combined EOF represents a synoptic pattern associated with the SACZ (South Atlantic convergence zone) and the third EOF is in spatial quadrature to the second EOF. The phase relationship of the EOFs, as computed from the principal components (PCs), suggests a nonlinear transition from the SACZ to the fully developed SAMS mode by November and between both components describing the SACZ by September-October (the rainy season onset). According to the LEC, the first mode is dominated by the eddy generation term at its maximum, the second by both baroclinic and eddy generation terms and the third by barotropic instability previous to the connection to the second mode by September-October. The predominance of the different LEC components at each phase of the SAMS can be used as an indicator of the onset of the rainy season in terms of physical processes, while the existence of the outstanding spectral peaks in the time dependence of the EOFs at the intraseasonal time scale could be used for monitoring purposes. Copyright (C) 2009 Royal Meteorological Society

PCA Tomography: how to extract information from data cubes

Astronomy has evolved almost exclusively by the use of spectroscopic and imaging techniques, operated separately. With the development of modern technologies, it is possible to obtain data cubes in which one combines both techniques simultaneously, producing images with spectral resolution. To extract information from them can be quite complex, and hence the development of new methods of data analysis is desirable. We present a method of analysis of data cube (data from single field observations, containing two spatial and one spectral dimension) that uses Principal Component Analysis (PCA) to express the data in the form of reduced dimensionality, facilitating efficient information extraction from very large data sets. PCA transforms the system of correlated coordinates into a system of uncorrelated coordinates ordered by principal components of decreasing variance. The new coordinates are referred to as eigenvectors, and the projections of the data on to these coordinates produce images we will call tomograms. The association of the tomograms (images) to eigenvectors (spectra) is important for the interpretation of both. The eigenvectors are mutually orthogonal, and this information is fundamental for their handling and interpretation. When the data cube shows objects that present uncorrelated physical phenomena, the eigenvector`s orthogonality may be instrumental in separating and identifying them. By handling eigenvectors and tomograms, one can enhance features, extract noise, compress data, extract spectra, etc. We applied the method, for illustration purpose only, to the central region of the low ionization nuclear emission region (LINER) galaxy NGC 4736, and demonstrate that it has a type 1 active nucleus, not known before. Furthermore, we show that it is displaced from the centre of its stellar bulge.

SIZE AS A LINE OF LEAST RESISTANCE II: DIRECT SELECTION ON SIZE OR CORRELATED RESPONSE DUE TO CONSTRAINTS?

Evolutionary change in New World Monkey (NWM) skulls occurred primarily along the line of least resistance defined by size (including allometric) variation (g(max)). Although the direction of evolution was aligned with this axis, it was not clear whether this macroevolutionary pattern results from the conservation of within population genetic covariance patterns (long-term constraint) or long-term selection along a size dimension, or whether both, constraints and selection, were inextricably involved. Furthermore, G-matrix stability can also be a consequence of selection, which implies that both, constraints embodied in g(max) and evolutionary changes observed on the trait averages, would be influenced by selection Here, we describe a combination of approaches that allows one to test whether any particular instance of size evolution is a correlated by-product due to constraints (g(max)) or is due to direct selection on size and apply it to NWM lineages as a case study. The approach is based on comparing the direction and amount of evolutionary change produced by two different simulated sets of net-selection gradients (beta), a size (isometric and allometric size) and a nonsize set. Using this approach it is possible to distinguish between the two hypotheses (indirect size evolution due to constraints or direct selection on size), because although both may produce an evolutionary response aligned with g(max), the amount of change produced by random selection operating through the variance/covariance patterns (constraints hypothesis) will be much smaller than that produced by selection on size (selection hypothesis). Furthermore, the alignment of simulated evolutionary changes with g(max) when selection is not on size is not as tight as when selection is actually on size, allowing a statistical test of whether a particular observed case of evolution along the line of least resistance is the result of selection along it or not. Also, with matrix diagonalization (principal components [PC]) it is possible to calculate directly the net-selection gradient on size alone (first PC [PC1]) by dividing the amount of phenotypic difference between any two populations by the amount of variation in PC1, which allows one to benchmark whether selection was on size or not