Practical Large-Scale Spatio-Temporal Modeling of Particulate Matter Concentrations

The last two decades have seen intense scientific and regulatory interest in the health effects of particulate matter (PM). Influential epidemiological studies that characterize chronic exposure of individuals rely on monitoring data that are sparse in space and time, so they often assign the same exposure to participants in large geographic areas and across time. We estimate monthly PM during 1988-2002 in a large spatial domain for use in studying health effects in the Nurses' Health Study. We develop a conceptually simple spatio-temporal model that uses a rich set of covariates. The model is used to estimate concentrations of PM10 for the full time period and PM2.5 for a subset of the period. For the earlier part of the period, 1988-1998, few PM2.5 monitors were operating, so we develop a simple extension to the model that represents PM2.5 conditionally on PM10 model predictions. In the epidemiological analysis, model predictions of PM10 are more strongly associated with health effects than when using simpler approaches to estimate exposure. Our modeling approach supports the application in estimating both fine-scale and large-scale spatial heterogeneity and capturing space-time interaction through the use of monthly-varying spatial surfaces. At the same time, the model is computationally feasible, implementable with standard software, and readily understandable to the scientific audience. Despite simplifying assumptions, the model has good predictive performance and uncertainty characterization.

The rice genome project in Japan

Since 1991, the Rice Genome Research Program in Japan has carried out rice genomics, such as large-scale cDNA analysis, construction of a fine-scale restriction fragment length polymorphism map, and physical mapping of the rice genome with yeast artificial chromosome clones. These studies have made a great impact on research into grass genomes and made rice a model plant for other cereal crop research. Starting in 1998, the Rice Genome Research Program will step into a new stage of genomics—that of genome sequencing. This project eventually should reveal all of the genomic sequence information in the rice plant and be an indispensable aid in understanding the genomics of other grass species.

Mapping and characterising subtropical estuarine landscapes using aerial photography and GIS for potential application in wildlife conservation and management

Coarse-resolution thematic maps derived from remotely sensed data and implemented in GIS play an important role in coastal and marine conservation, research and management. Here, we describe an approach for fine-resolution mapping of land-cover types using aerial photography and ancillary GIs and ground data in a large (100 x 35 km) subtropical estuarine system (Moreton Bay, Queensland, Australia). We have developed and implemented a classification scheme representing 24 coastal (subtidal, intertidal. mangrove, supratidal and terrestrial) cover types relevant to the ecology of estuarine animals, nekton and shorebirds. The accuracy of classifications of the intertidal and subtidal cover types, as indicated by the agreement between the mapped (predicted) and reference (ground) data, was 77-88%, depending on the zone and level of generalization required. The variability and spatial distribution of habitat mosaics (landscape types) across the mapped environment were assessed using K-means clustering and validated with Classification and Regression Tree models. Seven broad landscape types could be distinguished and ways of incorporating the information on landscape composition into site-specific conservation and field research are discussed. This research illustrates the importance and potential applications of fine-resolution mapping for conservation and management of estuarine habitats and their terrestrial and aquatic wildlife. (c) 2005 Elsevier Ltd. All rights reserved.

Modelling pre-clearing vegetation distribution using GIS-integrated statistical, ecological and data models: A case study from the wet tropics of Northeastern Australia

Traditional vegetation mapping methods use high cost, labour-intensive aerial photography interpretation. This approach can be subjective and is limited by factors such as the extent of remnant vegetation, and the differing scale and quality of aerial photography over time. An alternative approach is proposed which integrates a data model, a statistical model and an ecological model using sophisticated Geographic Information Systems (GIS) techniques and rule-based systems to support fine-scale vegetation community modelling. This approach is based on a more realistic representation of vegetation patterns with transitional gradients from one vegetation community to another. Arbitrary, though often unrealistic, sharp boundaries can be imposed on the model by the application of statistical methods. This GIS-integrated multivariate approach is applied to the problem of vegetation mapping in the complex vegetation communities of the Innisfail Lowlands in the Wet Tropics bioregion of Northeastern Australia. The paper presents the full cycle of this vegetation modelling approach including sampling sites, variable selection, model selection, model implementation, internal model assessment, model prediction assessments, models integration of discrete vegetation community models to generate a composite pre-clearing vegetation map, independent data set model validation and model prediction's scale assessments. An accurate pre-clearing vegetation map of the Innisfail Lowlands was generated (0.83r(2)) through GIS integration of 28 separate statistical models. This modelling approach has good potential for wider application, including provision of. vital information for conservation planning and management; a scientific basis for rehabilitation of disturbed and cleared areas; a viable method for the production of adequate vegetation maps for conservation and forestry planning of poorly-studied areas. (c) 2006 Elsevier B.V. All rights reserved.

Mach Bands: multi-scale spatial filtering and co-operative coding of edges and bars

Perception of Mach bands may be explained by spatial filtering ('lateral inhibition') that can be approximated by 2nd derivative computation, and several alternative models have been proposed. To distinguish between them, we used a novel set of ‘generalised Gaussian’ images, in which the sharp ramp-plateau junction of the Mach ramp was replaced by smoother transitions. The images ranged from a slightly blurred Mach ramp to a Gaussian edge and beyond, and also included a sine-wave edge. The probability of seeing Mach Bands increased with the (relative) sharpness of the junction, but was largely independent of absolute spatial scale. These data did not fit the predictions of MIRAGE, nor 2nd derivative computation at a single fine scale. In experiment 2, observers used a cursor to mark features on the same set of images. Data on perceived position of Mach bands did not support the local energy model. Perceived width of Mach bands was poorly explained by a single-scale edge detection model, despite its previous success with Mach edges (Wallis & Georgeson, 2009, Vision Research, 49, 1886-1893). A more successful model used separate (odd and even) scale-space filtering for edges and bars, local peak detection to find candidate features, and the MAX operator to compare odd- and even-filter response maps (Georgeson, VSS 2006, Journal of Vision 6(6), 191a). Mach bands are seen when there is a local peak in the even-filter (bar) response map, AND that peak value exceeds corresponding responses in the odd-filter (edge) maps.

Open-source mapping and services for Web-based land-cover validation

Monitoring land-cover changes on sites of conservation importance allows environmental problems to be detected, solutions to be developed and the effectiveness of actions to be assessed. However, the remoteness of many sites or a lack of resources means these data are frequently not available. Remote sensing may provide a solution, but large-scale mapping and change detection may not be appropriate, necessitating site-level assessments. These need to be easy to undertake, rapid and cheap. We present an example of a Web-based solution based on free and open-source software and standards (including PostGIS, OpenLayers, Web Map Services, Web Feature Services and GeoServer) to support assessments of land-cover change (and validation of global land-cover maps). Authorised users are provided with means to assess land-cover visually and may optionally provide uncertainty information at various levels: from a general rating of their confidence in an assessment to a quantification of the proportions of land-cover types within a reference area. Versions of this tool have been developed for the TREES-3 initiative (Simonetti, Beuchle and Eva, 2011). This monitors tropical land-cover change through ground-truthing at latitude / longitude degree confluence points, and for monitoring of change within and around Important Bird Areas (IBAs) by Birdlife International and the Royal Society for the Protection of Birds (RSPB). In this paper we present results from the second of these applications. We also present further details on the potential use of the land-cover change assessment tool on sites of recognised conservation importance, in combination with NDVI and other time series data from the eStation (a system for receiving, processing and disseminating environmental data). We show how the tool can be used to increase the usability of earth observation data by local stakeholders and experts, and assist in evaluating the impact of protection regimes on land-cover change.

The relationship between vegetation and modern pollen assemblages on Mount Paggeo (NE Greece)

In this study, we investigated the relationship between vegetation and modern-pollen rain along the elevational gradient of Mount Paggeo. We apply multivariate data analysis to assess the relationship between vegetation and modern-pollen rain and quantify the representativeness of forest zones. This study represents the first statistical analysis of pollen-vegetation relationship along an elevational gradient in Greece. Hence, this paper improves confidence in interpretation of palynological records from north-eastern Greece and may refine past climate reconstructions for a more accurate comparison of data and modelling. Numerical classification and ordination were performed on pollen data to assess differences among plant communities that beech (Fagus sylvatica) dominates or co-dominates. The results show a strong relationship between altitude, arboreal cover, human impact and variations in pollen and nonpollen palynomorph taxa percentages.

Linking environmental variables with regional- scale variability in ecological structure and standing stock of carbon within UK kelp forests

Kelp forests represent some of the most productive and diverse habitats on Earth. Understanding drivers of ecological patterns at large spatial scales is critical for effective management and conservation of marine habitats. We surveyed kelp forests dominated by Laminaria hyperborea (Gunnerus) Foslie 1884 across 9° latitude and >1000 km of coastline and measured a number of physical parameters at multiple scales to link ecological structure and standing stock of carbon with environmental variables. Kelp density, biomass, morphology and age were generally greater in exposed sites within regions, highlighting the importance of wave exposure in structuring L. hyperborea populations. At the regional scale, wave-exposed kelp canopies in the cooler regions (the north and west of Scotland) were greater in biomass, height and age than in warmer regions (southwest Wales and England). The range and maximal values of estimated standing stock of carbon contained within kelp forests was greater than in historical studies, suggesting that this ecosystem property may have been previously undervalued. Kelp canopy density was positively correlated with large-scale wave fetch and fine-scale water motion, whereas kelp canopy biomass and the standing stock of carbon were positively correlated with large-scale wave fetch and light levels and negatively correlated with temperature. As light availability and summer temperature were important drivers of kelp forest biomass, effective management of human activities that may affect coastal water quality is necessary to maintain ecosystem functioning, while increased temperatures related to anthropogenic climate change may impact the structure of kelp forests and the ecosystem services they provide.

Linking environmental variables with regional- scale variability in ecological structure and standing stock of carbon within UK kelp forests

Kelp forests represent some of the most productive and diverse habitats on Earth. Understanding drivers of ecological patterns at large spatial scales is critical for effective management and conservation of marine habitats. We surveyed kelp forests dominated by Laminaria hyperborea (Gunnerus) Foslie 1884 across 9° latitude and >1000 km of coastline and measured a number of physical parameters at multiple scales to link ecological structure and standing stock of carbon with environmental variables. Kelp density, biomass, morphology and age were generally greater in exposed sites within regions, highlighting the importance of wave exposure in structuring L. hyperborea populations. At the regional scale, wave-exposed kelp canopies in the cooler regions (the north and west of Scotland) were greater in biomass, height and age than in warmer regions (southwest Wales and England). The range and maximal values of estimated standing stock of carbon contained within kelp forests was greater than in historical studies, suggesting that this ecosystem property may have been previously undervalued. Kelp canopy density was positively correlated with large-scale wave fetch and fine-scale water motion, whereas kelp canopy biomass and the standing stock of carbon were positively correlated with large-scale wave fetch and light levels and negatively correlated with temperature. As light availability and summer temperature were important drivers of kelp forest biomass, effective management of human activities that may affect coastal water quality is necessary to maintain ecosystem functioning, while increased temperatures related to anthropogenic climate change may impact the structure of kelp forests and the ecosystem services they provide.

Predators on private land: broad-scale socioeconomic interactions influence large predator management

The proliferation of private land conservation areas (PLCAs) is placing increasing pressure on conservation authorities to effectively regulate their ecological management. Many PLCAs depend on tourism for income, and charismatic large mammal species are considered important for attracting international visitors. Broad-scale socioeconomic factors therefore have the potential to drive fine-scale ecological management, creating a systemic scale mismatch that can reduce long-term sustainability in cases where economic and conservation objectives are not perfectly aligned. We assessed the socioeconomic drivers and outcomes of large predator management on 71 PLCAs in South Africa. Owners of PLCAs that are stocking free-roaming large predators identified revenue generation as influencing most or all of their management decisions, and rated profit generation as a more important objective than did the owners of PLCAs that did not stock large predators. Ecotourism revenue increased with increasing lion (Panthera leo) density, which created a potential economic incentive for stocking lion at high densities. Despite this potential mismatch between economic and ecological objectives, lion densities were sustainable relative to available prey. Regional-scale policy guidelines for free-roaming lion management were ecologically sound. By contrast, policy guidelines underestimated the area required to sustain cheetah (Acinonyx jubatus), which occurred at unsustainable densities relative to available prey. Evidence of predator overstocking included predator diet supplementation and frequent reintroduction of game. We conclude that effective facilitation of conservation on private land requires consideration of the strong and not necessarily beneficial multiscale socioeconomic factors that influence private land management.

Transition to chaotic scattering: Signatures in the differential cross section

We show that bifurcations in chaotic scattering manifest themselves through the appearance of an infinitely fine-scale structure of singularities in the cross section. These ""rainbow singularities"" are created in a cascade, which is closely related to the bifurcation cascade undergone by the set of trapped orbits (the chaotic saddle). This cascade provides a signature in the differential cross section of the complex pattern of bifurcations of orbits underlying the transition to chaotic scattering. We show that there is a power law with a universal coefficient governing the sequence of births of rainbow singularities and we verify this prediction by numerical simulations.

Phylogeography of Chelonus insularis (Hymenoptera: Braconidae) and Campoletis sonorensis (Hymenoptera: Ichneumonidae), Two Primary Neotropical Parasitoids of the Fall Armyworm (Lepidoptera: Noctuidae)

In a previous study, we observed no spatial genetic structure in Mexican populations of the parasitoids Chelonus insularis Cresson (Hymenoptera: Braconidae) and Campoletis sonorensis Cameron (Hymenoptera: Ichneumonidae) by using microsatellite markers In the current study, we Investigated whether for these important parasitoids of the fall armyworm (Lepidoptera: Noctuidae) there is any genetic structure at a larger scale Insects of both species were collected across the American continent and their phylogeography was Investigated using both nuclear and mitochondria] markers Our results suggest an ancient north-south migration of C insularis, whereas no clear pattern] could be determined for C sonorensis. Nonetheless, the resulting topology indicated the existence of a cryptic taxon within this later species. a few Canadian specimens determined as C. sonorensis branch outside a clack composed of the Argentinean Chelonus grioti Blanchard, the Brazilian Chelonus flavicincta Ashmead, and the rest of the C sonorensis individuals The individuals revealing the cryptic taxon were collected from Thichoplusia in (Hubner) (Lepidoptera. Noctuidae) on tomato (Lycopersicon spp) and may represent a biotype that has adapted to the early season phenology of its host. Overall, the loosely defined spatial genetic structure previously shown at a local fine scale also was found at the larger scale, for both species Dispersal of these insects may be partly driven by wind as suggested by genetic similarities between Individuals coming from very distant locations.

Vector within-host feeding preference mediates transmission of a heterogeneously distributed pathogen

2. We documented the within-host distribution of two vector species that differ in transmission efficiency, the leafhoppers Draeculacephala minerva and Graphocephala atropunctata, and which are free to move throughout entirely caged alfalfa plants. The more efficient vector D. minerva fed preferentially at the base of the plant near the soil surface, whereas the less efficient G. atropunctata preferred overwhelming the top of the plant. 3. Next we documented X. fastidiosa heterogeneity in mechanically inoculated plants. Infection rates were up to 50% higher and mean bacterial population densities were 100-fold higher near the plant base than at the top or in the taproot. 4. Finally, we estimated transmission efficiency of the two leafhoppers when they were confined at either the base or top of inoculated alfalfa plants. Both vectors were inefficient when confined at the top of infected plants and were 20-60% more efficient when confined at the plant base. 5. These results show that vector transmission efficiency is determined by the interaction between leafhopper within-plant feeding behaviour and pathogen within-plant distribution. Fine-scale vector and pathogen overlap is likely to be a requirement generally for efficient transmission of vector-borne pathogens.

Sporadic and familial pheochromocytomas are associated with loss of at least two discrete intervals on chromosome 1p

Pheochromocytomas are tumors of the adrenal medulla originating in the chromaffin cells derived from the neural crest. Ten % of these tumors are associated with the familial cancer syndromes multiple endocrine neoplasia type 2, von Hippel-Lindau disease (VHL), and rarely, neurofibromatosis type 1, in which germ-line mutations have been identified in RET, VHL, and NF1, respectively. In both the sporadic and familial forms of pheochromocytoma, allelic loss at 1p, 3p, 17p, and 22q has been reported, yet the molecular pathogenesis of these tumors is largely unknown. Allelic loss at chromosome 1p has also been reported in other endocrine tumors, such as medullary thyroid cancer and tumors of the parathyroid gland, as well as in tumors of neural crest origin including neuroblastoma and malignant melanoma, In this study, we performed fine structure mapping of deletions at chromosome 1p in familial and sporadic pheochromocytomas to identify discrete regions likely housing tumor suppressor genes involved in the development of these tumors. Ten microsatellite markers spanning a region of similar to 70 cM (Ipter to 1p34.3) were used to screen 20 pheochromocytomas from 19 unrelated patients for loss of heterozygosity (LOH). LOH was detected at five or more loci in 8 of 13 (61%)sporadic samples and at five or more loci in four of five (80%) tumor samples from patients with multiple endocrine neoplasia type 2. No LOH at 1p was detected in pheochromocytomas from two VHL patients, Analysis of the combined sporadic and familial tumor data suggested three possible regions of common somatic loss, designated as PCI (D1S243 to D1S244), PC2 (D1S228 to D1S507), and PC3 (D1S507 toward the centromere). We propose that chromosome Ip may be the site of at least three putative tumor suppressor loci involved in the tumorigenesis of pheochromocytomas. At least one of these loci, PC2 spanning an interval of <3.8 cM, is Likely to have a broader role in the development of endocrine malignancies.

Assessment of factors that confound MRI and neuropathological correlation of human postmortem brain tissue

In spite of considerable technical advance in MRI techniques, the optical resolution of these methods are still limited. Consequently, the delineation of cytoarchitectonic fields based on probabilistic maps and brain volume changes, as well as small-scale changes seen in MRI scans need to be verified by neuronanatomical/neuropathological diagnostic tools. To attend the current interdisciplinary needs of the scientific community, brain banks have to broaden their scope in order to provide high quality tissue suitable for neuroimaging- neuropathology/anatomy correlation studies. The Brain Bank of the Brazilian Aging Brain Research Group (BBBABSG) of the University of Sao Paulo Medical School (USPMS) collaborates with researchers interested in neuroimaging-neuropathological correlation studies providing brains submitted to postmortem MRI in-situ. In this paper we describe and discuss the parameters established by the BBBABSG to select and to handle brains for fine-scale neuroimaging-neuropathological correlation studies, and to exclude inappropriate/unsuitable autopsy brains. We tried to assess the impact of the postmortem time and storage of the corpse on the quality of the MRI scans and to establish fixation protocols that are the most appropriate to these correlation studies. After investigation of a total of 36 brains, postmortem interval and low body temperature proved to be the main factors determining the quality of routine MRI protocols. Perfusion fixation of the brains after autopsy by mannitol 20% followed by formalin 20% was the best method for preserving the original brain shape and volume, and for allowing further routine and immunohistochemical staining. Taken to together, these parameters offer a methodological progress in screening and processing of human postmortem tissue in order to guarantee high quality material for unbiased correlation studies and to avoid expenditures by post-imaging analyses and histological processing of brain tissue.