Parallel Monte Carlo sampling scheme for sphere and hemisphere

The sampling of certain solid angle is a fundamental operation in realistic image synthesis, where the rendering equation describing the light propagation in closed domains is solved. Monte Carlo methods for solving the rendering equation use sampling of the solid angle subtended by unit hemisphere or unit sphere in order to perform the numerical integration of the rendering equation. In this work we consider the problem for generation of uniformly distributed random samples over hemisphere and sphere. Our aim is to construct and study the parallel sampling scheme for hemisphere and sphere. First we apply the symmetry property for partitioning of hemisphere and sphere. The domain of solid angle subtended by a hemisphere is divided into a number of equal sub-domains. Each sub-domain represents solid angle subtended by orthogonal spherical triangle with fixed vertices and computable parameters. Then we introduce two new algorithms for sampling of orthogonal spherical triangles. Both algorithms are based on a transformation of the unit square. Similarly to the Arvo's algorithm for sampling of arbitrary spherical triangle the suggested algorithms accommodate the stratified sampling. We derive the necessary transformations for the algorithms. The first sampling algorithm generates a sample by mapping of the unit square onto orthogonal spherical triangle. The second algorithm directly compute the unit radius vector of a sampling point inside to the orthogonal spherical triangle. The sampling of total hemisphere and sphere is performed in parallel for all sub-domains simultaneously by using the symmetry property of partitioning. The applicability of the corresponding parallel sampling scheme for Monte Carlo and Quasi-D/lonte Carlo solving of rendering equation is discussed.

A data forest: multi-dimensional visualization

As Terabyte datasets become the norm, the focus has shifted away from our ability to produce and store ever larger amounts of data, onto its utilization. It is becoming increasingly difficult to gain meaningful insights into the data produced. Also many forms of the data we are currently producing cannot easily fit into traditional visualization methods. This paper presents a new and novel visualization technique based on the concept of a Data Forest. Our Data Forest has been designed to be used with vir tual reality (VR) as its presentation method. VR is a natural medium for investigating large datasets. Our approach can easily be adapted to be used in a variety of different ways, from a stand alone single user environment to large multi-user collaborative environments. A test application is presented using multi-dimensional data to demonstrate the concepts involved.

Data forest: a collaborative version

As we increase our ability to produce and store ever larger amounts of data, it is becoming increasingly difficult to understand what the data is trying to tell us. Not all the data we are currently producing can easily fit into traditional visualization methods. This paper presents a new and novel visualization technique based on the concept of a Data Forest. Our Data Forest has been developed to be utilised by virtual reality (VR) systems. VR is a natural information medium. This approach can easily be adapted to be used in collaborative environments. A test application has been developed to demonstrate the concepts involved and a collaborative version tested.

Sampling series for determination of probability density of CDMA multiple access interference

Consideration is given to a standard CDMA system and determination of the density function of the interference with and without Gaussian noise using sampling theory concepts. The formula derived provides fast and accurate results and is a simple, useful alternative to other methods

Can REDD+ reconcile local priorities and needs with global mitigation benefits? lessons from Angai Forest, Tanzania

The scope of the reducing emissions from deforestation and forest degradation (REDD) mechanism has broadened REDD+ to accommodate different country interests such as natural forests, protected areas, as well as forests under community-based management. In Tanzania the REDD+ mechanism is still under development and pilot projects are at an early stage. In this paper, we seek to understand how local priorities and needs could be met in REDD+ implementation and how these expectations match with global mitigation benefits. We examine the local priorities and needs in the use of land and forest resources in the Angai Villages Land Forest Reserve (AVLFR) in the Liwale District of Lindi Region in Tanzania. Primary data was collected in two villages, Mihumo and Lilombe, using semistructured key informant interviews and participatory rural appraisal methods. In addition, the key informant interviews were conducted with other village, district, and national level actors, as well as international donors. Findings show that in the two communities REDD+ is seen as something new and is generating new expectations among communities. However, the Angai villagers highlight three key priorities that have yet to be integrated into the design of REDD+: water scarcity, rural development, and food security. At the local level improved forest governance and sustainable management of forest resources have been identified as one way to achieve livelihood diversification. Although the national goals of REDD+ include poverty reduction, these goals are not necessarily conducive to the goals of these communities. There exist both structural and cultural limits to the ability of the Angai villages to implement these goals and to improve forestry governance. Given the vulnerability to current and future climate variability and change it will be important to consider how the AVLFR will be managed and for whose benefit?

Differentiation between Neotropical rainforest, dry forest and savannah ecosystems by their modern pollen spectra and implications for the fossil pollen record

Accurate differentiation between tropical forest and savannah ecosystems in the fossil pollen record is hampered by the combination of: i) poor taxonomic resolution in pollen identification, and ii) the high species diversity of many lowland tropical families, i.e. with many different growth forms living in numerous environmental settings. These barriers to interpreting the fossil record hinder our understanding of the past distributions of different Neotropical ecosystems and consequently cloud our knowledge of past climatic, biodiversity and carbon storage patterns. Modern pollen studies facilitate an improved understanding of how ecosystems are represented by the pollen their plants produce and therefore aid interpretation of fossil pollen records. To understand how to differentiate ecosystems palynologically, it is essential that a consistent sampling method is used across ecosystems. However, to date, modern pollen studies from tropical South America have employed a variety of methodologies (e.g. pollen traps, moss polsters, soil samples). In this paper, we present the first modern pollen study from the Neotropics to examine the modern pollen rain from moist evergreen tropical forest (METF), semi-deciduous dry tropical forest (SDTF) and wooded savannah (cerradão) using a consistent sampling methodology (pollen traps). Pollen rain was sampled annually in September for the years 1999–2001 from within permanent vegetation study plots in, or near, the Noel Kempff Mercado National Park (NKMNP), Bolivia. Comparison of the modern pollen rain within these plots with detailed floristic inventories allowed estimates of the relative pollen productivity and dispersal for individual taxa to be made (% pollen/% vegetation or ‘p/v’). The applicability of these data to interpreting fossil records from lake sediments was then explored by comparison with pollen assemblages obtained from five lake surface samples.

Evidence of increased net ecosystem productivity associated with a longer vegetated season in a deciduous forest in south-central Indiana, USA

Observations of net ecosystem exchange (NEE) of carbon and its biophysical drivers have been collected at the AmeriFlux site in the Morgan-Monroe State Forest (MMSF) in Indiana, USA since 1998. Thus, this is one of the few deciduous forest sites in the world, where a decadal analysis on net ecosystem productivity (NEP) trends is possible. Despite the large interannual variability in NEP, the observations show a significant increase in forest productivity over the past 10 years (by an annual increment of about 10 g C m−2 yr−1). There is evidence that this trend can be explained by longer vegetative seasons, caused by extension of the vegetative activity in the fall. Both phenological and flux observations indicate that the vegetative season extended later in the fall with an increase in length of about 3 days yr−1 for the past 10 years. However, these changes are responsible for only 50% of the total annual gain in forest productivity in the past decade. A negative trend in air and soil temperature during the winter months may explain an equivalent increase in NEP through a decrease in ecosystem respiration.

An assessment of observed vertical flux divergence in long-term eddy-covariance measurements over two Midwestern forest ecosystems

Vertical divergence of CO2 fluxes is observed over two Midwestern AmeriFlux forest sites. The differences in ensemble averaged hourly CO2 fluxes measured at two heights above canopy are relatively small (0.2–0.5 μmol m−2 s−1), but they are the major contributors to differences (76–256 g C m−2 or 41.8–50.6%) in estimated annual net ecosystem exchange (NEE) in 2001. A friction velocity criterion is used in these estimates but mean flow advection is not accounted for. This study examines the effects of coordinate rotation, averaging time period, sampling frequency and co-spectral correction on CO2 fluxes measured at a single height, and on vertical flux differences measured between two heights. Both the offset in measured vertical velocity and the downflow/upflow caused by supporting tower structures in upwind directions lead to systematic over- or under-estimates of fluxes measured at a single height. An offset of 1 cm s−1 and an upflow/downflow of 1° lead to 1% and 5.6% differences in momentum fluxes and nighttime sensible heat and CO2 fluxes, respectively, but only 0.5% and 2.8% differences in daytime sensible heat and CO2 fluxes. The sign and magnitude of both offset and upflow/downflow angle vary between sonic anemometers at two measurement heights. This introduces a systematic and large bias in vertical flux differences if these effects are not corrected in the coordinate rotation. A 1 h averaging time period is shown to be appropriate for the two sites. In the daytime, the absolute magnitudes of co-spectra decrease with height in the natural frequencies of 0.02–0.1 Hz but increase in the lower frequencies (<0.01 Hz). Thus, air motions in these two frequency ranges counteract each other in determining vertical flux differences, whose magnitude and sign vary with averaging time period. At night, co-spectral densities of CO2 are more positive at the higher levels of both sites in the frequency range of 0.03–0.4 Hz and this vertical increase is also shown at most frequencies lower than 0.03 Hz. Differences in co-spectral corrections at the two heights lead to a positive shift in vertical CO2 flux differences throughout the day at both sites. At night, the vertical CO2 flux differences between two measurement heights are 20–30% and 40–60% of co-spectral corrected CO2 fluxes measured at the lower levels of the two sites, respectively. Vertical differences of CO2 flux are relatively small in the daytime. Vertical differences in estimated mean vertical advection of CO2 between the two measurement heights generally do not improve the closure of the 1D (vertical) CO2 budget in the air layer between the two measurement heights. This may imply the significance of horizontal advection. However, a reliable assessment of mean advection contributions in annual NEE estimate at these two AmeriFlux sites is currently an unsolved problem.

Advanced feature selection methods in multinominal dementia classification from structural MRI data

Recent studies showed that features extracted from brain MRIs can well discriminate Alzheimer’s disease from Mild Cognitive Impairment. This study provides an algorithm that sequentially applies advanced feature selection methods for findings the best subset of features in terms of binary classification accuracy. The classifiers that provided the highest accuracies, have been then used for solving a multi-class problem by the one-versus-one strategy. Although several approaches based on Regions of Interest (ROIs) extraction exist, the prediction power of features has not yet investigated by comparing filter and wrapper techniques. The findings of this work suggest that (i) the IntraCranial Volume (ICV) normalization can lead to overfitting and worst the accuracy prediction of test set and (ii) the combined use of a Random Forest-based filter with a Support Vector Machines-based wrapper, improves accuracy of binary classification.

Molecular species delimitation of a symbiotic fig-pollinating wasp species complex reveals extreme deviation from reciprocal partner specificity

Background: Symbiotic relationships have contributed to major evolutionary innovations, the maintenance of fundamental ecosystem functions, and the generation and maintenance of biodiversity. However, the exact nature of host/symbiont associations, which has important consequences for their dynamics, is often poorly known due to limited understanding of symbiont taxonomy and species diversity. Among classical symbioses, figs and their pollinating wasps constitute a highly diverse keystone resource in tropical forest and savannah environments. Historically, they were considered to exemplify extreme reciprocal partner specificity (one-to-one host-symbiont species relationships), but recent work has revealed several more complex cases. However, there is a striking lack of studies with the specific aims of assessing symbiont diversity and how this varies across the geographic range of the host. Results: Here, we use molecular methods to investigate cryptic diversity in the pollinating wasps of a widespread Australian fig species. Standard barcoding genes and methods were not conclusive, but incorporation of phylogenetic analyses and a recently developed nuclear barcoding gene (ITS2), gave strong support for five pollinator species. Each pollinator species was most common in a different geographic region, emphasising the importance of wide geographic sampling to uncover diversity, and the scope for divergence in coevolutionary trajectories across the host plant range. In addition, most regions had multiple coexisting pollinators, raising the question of how they coexist in apparently similar or identical resource niches. Conclusion: Our study offers a striking example of extreme deviation from reciprocal partner specificity over the full geographical range of a fig-wasp system. It also suggests that superficially identical species may be able to co-exist in a mutualistic setting albeit at different frequencies in relation to their fig host’s range. We show that comprehensive sampling and molecular taxonomic techniques may be required to uncover the true structure of cryptic biodiversity underpinning intimate ecological interactions.

Soil conditioning and plant-soil feedbacks in a modified forest ecosystem are soil-context dependent

Aims There is potential for altered plant-soil feedback (PSF) to develop in human-modified ecosystems but empirical data to test this idea are limited. Here, we compared the PSF operating in jarrah forest soil restored after bauxite mining in Western Australia with that operating in unmined soil. Methods Native seedlings of jarrah (Eucalyptus marginata), acacia (Acacia pulchella), and bossiaea (Bossiaea ornata) were grown in unmined and restored soils to measure conditioning of chemical and biological properties as compared with unplanted control soils. Subsequently, acacia and bossiaea were grown in soils conditioned by their own or by jarrah seedlings to determine the net PSF. Results In unmined soil, the three plant species conditioned the chemical properties but had little effect on the biological properties. In comparison, jarrah and bossiaea conditioned different properties of restored soil while acacia did not condition this soil. In unmined soil, neutral PSF was observed, whereas in restored soil, negative PSF was associated with acacia and bossiaea. Conclusions Soil conditioning was influenced by soil context and plant species. The net PSF was influenced by soil context, not by plant species and it was different in restored and unmined soils. The results have practical implications for ecosystem restoration after human activities.

Designing a sampling scheme to reveal correlations between weeds and soil properties at multiple spatial scales

Weeds tend to aggregate in patches within fields and there is evidence that this is partly owing to variation in soil properties. Because the processes driving soil heterogeneity operate at different scales, the strength of the relationships between soil properties and weed density would also be expected to be scale-dependent. Quantifying these effects of scale on weed patch dynamics is essential to guide the design of discrete sampling protocols for mapping weed distribution. We have developed a general method that uses novel within-field nested sampling and residual maximum likelihood (REML) estimation to explore scale-dependent relationships between weeds and soil properties. We have validated the method using a case study of Alopecurus myosuroides in winter wheat. Using REML, we partitioned the variance and covariance into scale-specific components and estimated the correlations between the weed counts and soil properties at each scale. We used variograms to quantify the spatial structure in the data and to map variables by kriging. Our methodology successfully captured the effect of scale on a number of edaphic drivers of weed patchiness. The overall Pearson correlations between A. myosuroides and soil organic matter and clay content were weak and masked the stronger correlations at >50 m. Knowing how the variance was partitioned across the spatial scales we optimized the sampling design to focus sampling effort at those scales that contributed most to the total variance. The methods have the potential to guide patch spraying of weeds by identifying areas of the field that are vulnerable to weed establishment.

Sampling and analyzing metals in soils for archaeological prospection: a critique

This paper presents a critique of current methods of sampling and analyzing soils for metals in archaeological prospection. Commonly used methodologies in soil science are shown to be suitable for archaeological investigations, with a concomitant improvement in their resolution. Understanding the soil-fraction location, concentration range, and spatial distribution of autochthonous (native) soil metals is shown to be a vital precursor to archaeological-site investigations, as this is the background upon which anthropogenic deposition takes place. Nested sampling is suggested as the most cost-effective method of investigating the spatial variability in the autochthonous metal concentrations. The use of the appropriate soil horizon (or sampling depth) and point sampling are critical in the preparation of a sampling regime. Simultaneous extraction is proposed as the most efficient method of identifying the location and eventual fate of autochthonous and anthropogenic metals, respectively.

Sampling uncertainty in gridded sea surface temperature products and Advanced Very High Resolution Radiometer (AVHRR) Global Area Coverage (GAC) data

Sea surface temperature (SST) data are often provided as gridded products, typically at resolutions of order 0.05 degrees from satellite observations to reduce data volume at the request of data users and facilitate comparison against other products or models. Sampling uncertainty is introduced in gridded products where the full surface area of the ocean within a grid cell cannot be fully observed because of cloud cover. In this paper we parameterise uncertainties in SST as a function of the percentage of clear-sky pixels available and the SST variability in that subsample. This parameterisation is developed from Advanced Along Track Scanning Radiometer (AATSR) data, but is applicable to all gridded L3U SST products at resolutions of 0.05-0.1 degrees, irrespective of instrument and retrieval algorithm, provided that instrument noise propagated into the SST is accounted for. We also calculate the sampling uncertainty of ~0.04 K in Global Area Coverage (GAC) Advanced Very High Resolution Radiometer (AVHRR) products, using related methods.

Forest-obligate Sabethes mosquitoes suggest palaeoecological perturbations

The origin of tropical forest diversity has been hotly debated for decades. Although specific mechanisms vary, many such explanations propose some vicariance in the distribution of species during glacial cycles and several have been supported by genetic evidence in Neotropical taxa. However, no consensus exists with regard to the extent or time frame of the vicariance events. Here, we analyse the cytochrome oxidase II mitochondrial gene of 250 Sabethes albiprivus B mosquitoes sampled from western Sao Paulo in Brazil. There was very low population structuring among collection sites (Phi(ST) = 0.03, P = 0.04). Historic demographic analyses and the contemporary geographic distribution of genetic diversity suggest that the populations sampled are not at demographic equilibrium. Three distinct mitochondrial clades were observed in the samples, one of which differed significantly in its geographic distribution relative to the other two within a small sampling area (similar to 70 x 35 km). This fact, supported by the inability of maximum likelihood analyses to achieve adequate fits to simple models for the population demography of the species, suggests a more complex history, possibly involving disjunct forest refugia. This hypothesis is supported by a genetic signal of recent population growth, which is expected if population sizes of this forest-obligate insect increased during the forest expansions that followed glacial periods. Although a time frame cannot be reliably inferred for the vicariance event leading to the three genetic clades, molecular clock estimates place this at similar to 1 Myr before present.