Classification method for disease risk mapping based on discrete hidden Markov random fields

Risk mapping in epidemiology enables areas with a low or high risk of disease contamination to be localized and provides a measure of risk differences between these regions. Risk mapping models for pooled data currently used by epidemiologists focus on the estimated risk for each geographical unit. They are based on a Poisson log-linear mixed model with a latent intrinsic continuous hidden Markov random field (HMRF) generally corresponding to a Gaussian autoregressive spatial smoothing. Risk classification, which is necessary to draw clearly delimited risk zones (in which protection measures may be applied), generally must be performed separately. We propose a method for direct classified risk mapping based on a Poisson log-linear mixed model with a latent discrete HMRF. The discrete hidden field (HF) corresponds to the assignment of each spatial unit to a risk class. The risk values attached to the classes are parameters and are estimated. When mapping risk using HMRFs, the conditional distribution of the observed field is modeled with a Poisson rather than a Gaussian distribution as in image segmentation. Moreover, abrupt changes in risk levels are rare in disease maps. The spatial hidden model should favor smoothed out risks, but conventional discrete Markov random fields (e.g. the Potts model) do not impose this. We therefore propose new potential functions for the HF that take into account class ordering. We use a Monte Carlo version of the expectation-maximization algorithm to estimate parameters and determine risk classes. We illustrate the method's behavior on simulated and real data sets. Our method appears particularly well adapted to localize high-risk regions and estimate the corresponding risk levels.     

Towards an atlas of human helminth infection in sub-Saharan Africa: the use of geographical information systems (GIS)

The value of a geographical perspective to infectious disease epidemiology and control has long been recognized. However, the labour required to produce maps, and keep them up to date, has inhibited the development of this area, and very little is currently known about the spatial distribution of parasitic infections other than malaria, trypanosomiasis and onchocerciasis. A recent initiative by an international group of collaborators is attempting to redress the absence of detailed spatial information on the major helminth infections of humans. In this article, Simon Brooker and colleagues describe progress made by this initiative in mapping helminth infections in sub-Saharan Africa, highlighting the value as well as the limitations of this empirical mapping approach.     

用GIS技术研究中国簇毛黄耆亚属（豆科：黄耆属）的地理分布式样

用ＧＩＳ技术设计和绘制了豆科黄耆属（Ａｓｔｒａｇａｌｕｓ Ｌ．）簇毛黄耆亚属在中中的地理分布图。以种类和县级分面为基本构图单元。分布图形均呈斑块状。分布式样提示出亚属是一个集中分布在横断山和喜马拉雅,适应于高寒山地的特化类群。根据地理公布直观图及有关统计分析,认为横断山是这个亚属的分布中心、分化中心和特有中心。公布式样和直观图还揭示出一些种之间、组之间有趣的替代现象。     

Studies on Geographical Distribution Pattern of the Subgenus Pogonophace (Fabaceae: Astragalus) in China Using GIS Technique

The geographical distribution maps of the subgenus Pogonophace (Fabaceae: Astragalus) in China were designed and drawn using GIS cartographic technique. The species of the subgenus and county of China were treated as the basic composition units in the GIS cartographic technique. Most of the distribution maps were shown in spots. The distribution pattern of the subgenus illustrates that it is a peculiar group to adapt the cold alpine environment and distribute mainly in Hengduan Mountains and Himalayas. According to the geographical distribution maps and some statistic analyses, Hengduan Mountains region is suggested to be the distribution center, differentiation center and endemic center of the subgenus. Some vicariance traces at levels of the species or sections are very interesting among the distribution patterns of the subgenus and shown clearly in the maps.     

Sensitivity of macroecological patterns of South American parrots to differences in data sources

A criticism of macroecological studies has been their extensive use of secondary data sources. In this note we evaluate how different data sources affect macroecological patterns for the parrots of South America. We mapped extents of parrot occurrence based on four sources of range maps. We compared basic statistics for geographical range size distribution (mean, variance and skew) and calculated correlations between geographical range size estimates and grid cell species richness estimates. Finally, results from multiple regression analyses of species richness against six environmental variables were also compared. We found that patterns were very robust to the data source, with only relatively slight quantitative differences. Our results reinforce the notion that patterns emerging from macroecological analyses are robust to variations in data sources and cannot be merely artefacts resulting from low data quality, notably poorly defined mapping and conflicting taxonomy.     

Land cover and tsetse fly distributions in sub-Saharan Africa

Abstract.  This study aims to provide trypanosomiasis-affected countries with standardized datasets and methodologies for mapping the habitat of the tsetse fly ( Glossina spp., the disease vector) by customizing and integrating state-of-the-art land cover maps on different spatial scales. Using a combination of inductive and deductive approaches, land cover and fly distribution maps are analysed in a geographic information system (GIS) to estimate the suitability of different land cover units for the three groups (subgenera) of Glossina. All land cover datasets used for and produced by the study comply with the Land Cover Classification System (LCCS). At the continental scale, a strong correlation between land cover and tsetse habitat is found for both the fusca and palpalis groups, whereas a weaker correlation found for the morsitans group may be indicative of less restrictive ecological requirements. At the regional and national levels, thematic aggregation of the multi-purpose Africover datasets yielded high-resolution, standardized land cover maps tailored for tsetse habitat for eight East African countries. The national maps provide remarkable spatial resolution, thematic detail and geographical coverage. They may be applied in subsequent phases of tsetse and trypanosomiasis control projects, including the planning of entomological surveys, actual tsetse control operations and planning for land use in reclaimed areas. The methodology and datasets discussed in the paper may have applications beyond the tsetse and trypanosomiasis issue and may be used with reference to other arthropod vectors, vector-borne and parasitic diseases.     

Type and spatial structure of distribution data and the perceived determinants of geographical gradients in ecology: the species richness of African birds

Aim Studies exploring the determinants of geographical gradients in the occurrence of species or their traits obtain data by: (1) overlaying species range maps; (2) mapping survey‐based species counts; or (3) superimposing models of individual species’ distributions. These data types have different spatial characteristics. We investigated whether these differences influence conclusions regarding postulated determinants of species richness patterns. Location Our study examined terrestrial bird diversity patterns in 13 nations of southern and eastern Africa, spanning temperate to tropical climates. Methods Four species richness maps were compiled based on range maps, field‐derived bird atlas data, logistic and autologistic distribution models. Ordinary and spatial regression models served to examine how well each of five hypotheses predicted patterns in each map. These hypotheses propose productivity, temperature, the heat–water balance, habitat heterogeneity and climatic stability as the predominant determinants of species richness. Results The four richness maps portrayed broadly similar geographical patterns but, due to the nature of underlying data types, exhibited marked differences in spatial autocorrelation structure. These differences in spatial structure emerged as important in determining which hypothesis appeared most capable of explaining each map's patterns. This was true even when regressions accounted for spurious effects of spatial autocorrelation. Each richness map, therefore, identified a different hypothesis as the most likely cause of broad‐scale gradients in species diversity. Main conclusions Because the ‘true’ spatial structure of species richness patterns remains elusive, firm conclusions regarding their underlying environmental drivers remain difficult. More broadly, our findings suggest that care should be taken to interpret putative determinants of large‐scale ecological gradients in light of the type and spatial characteristics of the underlying data. Indeed, closer scrutiny of these underlying data — here the distributions of individual species — and their environmental associations may offer important insights into the ultimate causes of observed broad‐scale patterns.     

The geography of body size – challenges of the interspecific approach

Recent compilations of large-scale data bases on the geographical distributions and body sizes of animals, coupled with developments in spatial statistics, have led to renewed interest in the geographical distribution of animal body sizes and the interspecific version of Bergmann's rule. Standard practice seems to be an examination of mean body sizes within higher taxa on gridded maps, with little regard to species richness or phylogeny. However, because the frequency distribution of body sizes is typically highly skewed, average size within grid cells may differ significantly between species-rich and species-poor cells even when the median and modal sizes remain constant. Species richness influences body size patterns because species are not added to communities at random in relation to their size: areas of low diversity are characterized by a higher range of body sizes than is expected by chance. Finally, a consideration of phylogenetic structure within taxa is necessary to elucidate whether patterns in the geography of size result from turnover between or within intermediate taxonomic levels. We suggest that the highest and lowest quantiles of body size distribution be mapped in order to expose possible physiological or ecological limitations on body size.     

The Geographical Distribution and Burden of Trachoma in Africa

Background

There remains a lack of epidemiological data on the geographical distribution of trachoma to support global mapping and scale up of interventions for the elimination of trachoma. The Global Atlas of Trachoma (GAT) was launched in 2011 to address these needs and provide standardised, updated and accessible maps. This paper uses data included in the GAT to describe the geographical distribution and burden of trachoma in Africa.

Methods

Data assembly used structured searches of published and unpublished literature to identify cross-sectional epidemiological data on the burden of trachoma since 1980. Survey data were abstracted into a standardised database and mapped using geographical information systems (GIS) software. The characteristics of all surveys were summarized by country according to data source, time period, and survey methodology. Estimates of the current population at risk were calculated for each country and stratified by endemicity class.

Results

At the time of writing, 1342 records are included in the database representing surveys conducted between 1985 and 2012. These data were provided by direct contact with national control programmes and academic researchers (67%), peer-reviewed publications (17%) and unpublished reports or theses (16%). Prevalence data on active trachoma are available in 29 of the 33 countries in Africa classified as endemic for trachoma, and 1095 (20.6%) districts have representative data collected through population-based prevalence surveys. The highest prevalence of active trachoma and trichiasis remains in the Sahel area of West Africa and Savannah areas of East and Central Africa and an estimated 129.4 million people live in areas of Africa confirmed to be trachoma endemic.

Conclusion

The Global Atlas of Trachoma provides the most contemporary and comprehensive summary of the burden of trachoma within Africa. The GAT highlights where future mapping is required and provides an important planning tool for scale-up and surveillance of trachoma control.     

A Scoping Review and Prevalence Analysis of Soil-Transmitted Helminth Infections in Honduras

Background

Honduras is endemic for soil-transmitted helminth (STH) infections, but critical information gaps still remain on the prevalence and intensity of these infections as well as on their spatial distribution at subnational levels.

Objectives

Firstly, to review the research activity on STH infections in Honduras and secondly, to carry out a national prevalence analysis and map the geographical distribution of these infections in children.

Methods

A systematic search was conducted of the published and grey literature to identify scientific work on the impact and prevalence of STH infections done between May 1930 and June 30, 2012. International databases and Honduran journals were searched. Grey literature was gleaned from local libraries and key informants. Select studies conducted between 2001 and 2012 were used to produce prevalence maps and to investigate association between STH prevalence and socio-economic and environmental factors.

Results

Of 257 identified studies, 211 (21.4% peer-reviewed) were retained for analysis and categorized as clinical research (10.9%), treatment efficacy studies (8.1%) or epidemiological studies (81%). Prevalence analysis and geographical mapping included 36 epidemiological studies from Honduras''s 18 departments and 23% of its municipalities. Overall STH prevalence was >50% in 40.6% of municipalities. Prevalences above 20% for each trichuriasis, ascariasis, and hookworm infection were found in 68%, 47.8%, and 7.2% of studied municipalities, respectively. Municipalities with lower human development index, less access to of potable water, and with higher annual precipitation showed higher STH prevalences.

Conclusions

This is the first study to provide a comprehensive historic review of STH research activity and prevalence in Honduras, revealing important knowledge gaps related to infection risk factors, disease burden, and anti-parasitic drug efficacy, among others. Our decade-long prevalence analysis reveals geographical differences in STH prevalence and these findings suggest that differential intervention strategies might be necessary in Honduras for the control of these infections.     

Assessment of the national schistosomiasis control program in a typical region along the Yangtze River,China

Schistosomiasis remains a major public health problem in eastern China, particularly along the Yangtze River Basin. The latest national schistosomiasis control program (NSCP) was implemented in 2005 with the main goal of reducing the rate of infection to less than 5% by 2008 and 1% by 2015. To assess the progress, we applied a Bayesian spatio-temporal model to describe dynamics of schistosomiasis in Guichi, Anhui Province, China, using annual parasitological and environmental data collected within 41 sample villages for the period 2005–2011. Predictive maps of schistosomiasis showed that the disease prevalence remains constant and low. Results of uncertainty analysis, in the form of probability contour maps (PCMs), indicated that the first goal of “infection rate less than 5% by 2008” was fully achieved in the study area. More longitudinal data for schistosomiasis are needed for the assessment of the second goal of “infection rate less than 1% by 2015”. Compared with the traditional way of mapping uncertainty (e.g., variance or mean-square error), our PCMs provide more realistic information for schistosomiasis control.     

县区生态系统服务分布图编制——以北京市延庆区土壤保持服务为例

地图是直观展示生态系统服务空间分布格局的手段,是确定重要生态保护目标和区域的主要方法。结合制图学理论方法及国家、行业相关制图规范,探讨生态系统服务分布图编制的目标、原则、流程和制图方法。以编制北京市延庆区1 ： 25万土壤保持服务分布图为例,分析了地理基础确定、地理要素取舍以及土壤保持服务分级等关键制图方法,提出了土壤保持服务分布图的编制规范。研究结果表明,编制的图件能够详尽的展示土壤保持服务的分布特征,精细的反映生态系统服务与自然、人文要素的关系。通过详实的图面信息可进一步判别土壤保持服务分布重要区域,这将为区域生态环境保护规划提供重要技术手段。     

Global mapping of infectious disease

The primary aim of this review was to evaluate the state of knowledge of the geographical distribution of all infectious diseases of clinical significance to humans. A systematic review was conducted to enumerate cartographic progress, with respect to the data available for mapping and the methods currently applied. The results helped define the minimum information requirements for mapping infectious disease occurrence, and a quantitative framework for assessing the mapping opportunities for all infectious diseases. This revealed that of 355 infectious diseases identified, 174 (49%) have a strong rationale for mapping and of these only 7 (4%) had been comprehensively mapped. A variety of ambitions, such as the quantification of the global burden of infectious disease, international biosurveillance, assessing the likelihood of infectious disease outbreaks and exploring the propensity for infectious disease evolution and emergence, are limited by these omissions. An overview of the factors hindering progress in disease cartography is provided. It is argued that rapid improvement in the landscape of infectious diseases mapping can be made by embracing non-conventional data sources, automation of geo-positioning and mapping procedures enabled by machine learning and information technology, respectively, in addition to harnessing labour of the volunteer ‘cognitive surplus’ through crowdsourcing.     

iMAR: An Interactive Web-Based Application for Mapping Herbicide Resistant Weeds

Herbicides are the major weed control tool in most cropping systems worldwide. However, the high reliance on herbicides has led to environmental issues as well as to the evolution of herbicide-resistant biotypes. Resistance is a major concern in modern agriculture and early detection of resistant biotypes is therefore crucial for its management and prevention. In this context, a timely update of resistance biotypes distribution is fundamental to devise and implement efficient resistance management strategies. Here we present an innovative web-based application called iMAR (interactive MApping of Resistance) for the mapping of herbicide resistant biotypes. It is based on open source software tools and translates into maps the data reported in the GIRE (Italian herbicide resistance working group) database of herbicide resistance at national level. iMAR allows an automatic, easy and cost-effective updating of the maps a nd provides two different systems, “static” and “dynamic”. In the first one, the user choices are guided by a hierarchical tree menu, whereas the latter is more flexible and includes a multiple choice criteria (type of resistance, weed species, region, cropping systems) that permits customized maps to be created. The generated information can be useful to various stakeholders who are involved in weed resistance management: farmers, advisors, national and local decision makers as well as the agrochemical industry. iMAR is freely available, and the system has the potential to handle large datasets and to be used for other purposes with geographical implications, such as the mapping of invasive plants or pests.     

A new forest cover map of continental southeast Asia derived from SPOT‐VEGETATION satellite imagery

Question: Can recent satellite imagery of coarse spatial resolution support forest cover assessment and mapping at the regional level? Location: Continental southeast Asia. Methods: Forest cover mapping was based on digital classification of SPOT4‐VEGETATION satellite images of 1 km spatial resolution from the dry seasons 1998/1999 and 1999/2000. Following a geographical stratification, the spectral clusters were visually assigned to land cover classes. The forest classes were validated by an independent set of maps, derived from interpretation of satellite imagery of high spatial resolution (Landsat TM, 30 m). Forest area estimates from the regional forest cover map were compared to the forest figures of the FAO database. Results: The regional forest cover map displays 12 forest and land cover classes. The mapping of the region's deciduous and fragmented forest cover remained challenging. A high correlation was found between forest area estimates obtained from this map and from the Landsat TM derived maps. The regional and sub‐regional forest area estimates were close to those reported by FAO. Conclusion: SPOT4‐VEGETATION satellite imagery can be used for mapping consistently and uniformly the extent and distribution of the broad forest cover types at the regional scale. The new map can be considered as an update and improvement on existing regional forest cover maps.     

How accurate are probability-based estimates of wetland extent? Results of a California validation study

Estimates of wetland and stream extent and distribution form the basis for state and federal monitoring and management programs and guide policy development decisions. The current default approach, comprehensive mapping, provides the most complete information on extent and distribution but is prohibitively expensive across large geographic areas. In contrast, probabilistic mapping produces statistical estimates of extent and distribution at a fraction of the cost of comprehensive mapping. This study provides a direct comparison to address how well probability-based estimates of wetland extent approximate results from comprehensive mapping, and the degree to which inter-mapper variability contributes to overall error in probability-based estimates. Two regions of California were selected based on existence of recent, comprehensive wetland and stream maps. Probabilistic sample plot locations were selected by generalized random tessellation stratified sampling and sample plot maps were produced from the same source imagery as the comprehensive maps. Sample maps were compared for inter-mapper variability, plot-by-plot differences between sample and comprehensive maps, and differences between sample estimates and comprehensive totals. On a plot-by-plot basis differences in mapped wetland area between comprehensive maps and probabilistic sample maps approached 50 % in either the positive or negative direction, leading to uncertainty in directly comparing maps derived from these two approaches. With application of standardized protocols and rigorous quality control measures, we were able to achieve a 97 % overall accuracy rate between independent mapping teams applying the probabilistic mapping approach. Our results suggest caution when comparing comprehensive and sample based wetland extent estimates and highlight the importance of mapper intercalibration.     

Some medical applications of the oxford scanning proton microprobe

Results from several medical investigations carried out using the Oxford scanning proton microprobe are presented, including maps of the hepatic copper-distribution in primary biliary cirrhosis and maps of the iron distribution in primary hemochromatosis. Preliminary studies of human nervous tissue reveal that morphologically recognizable structures can be differentiated using precision elemental mapping, and this may lead to a powerful new way of distinguishing subtle perturbations of structure and function. In further prelimianry studies, localized aluminum structures have been observed in Alzheimer’s disease tissue at bulk levels of less than parts per million.     

Mapping the Geographical Distribution of Lymphatic Filariasis in Zambia

Background

Past case reports have indicated that lymphatic filariasis (LF) occurs in Zambia, but knowledge about its geographical distribution and prevalence pattern, and the underlying potential environmental drivers, has been limited. As a background for planning and implementation of control, a country-wide mapping survey was undertaken between 2003 and 2011. Here the mapping activities are outlined, the findings across the numerous survey sites are presented, and the ecological requirements of the LF distribution are explored.

Methodology/Principal findings

Approximately 10,000 adult volunteers from 108 geo-referenced survey sites across Zambia were examined for circulating filarial antigens (CFA) with rapid format ICT cards, and a map indicating the distribution of CFA prevalences in Zambia was prepared. 78% of survey sites had CFA positive cases, with prevalences ranging between 1% and 54%. Most positive survey sites had low prevalence, but six foci with more than 15% prevalence were identified. The observed geographical variation in prevalence pattern was examined in more detail using a species distribution modeling approach to explore environmental requirements for parasite presence, and to predict potential suitable habitats over unsurveyed areas. Of note, areas associated with human modification of the landscape appeared to play an important role for the general presence of LF, whereas temperature (measured as averaged seasonal land surface temperature) seemed to be an important determinant of medium-high prevalence levels.

Conclusions/significance

LF was found to be surprisingly widespread in Zambia, although in most places with low prevalence. The produced maps and the identified environmental correlates of LF infection will provide useful guidance for planning and start-up of geographically targeted and cost-effective LF control in Zambia.     

Mapping and Modelling the Geographical Distribution and Environmental Limits of Podoconiosis in Ethiopia

Background

Ethiopia is assumed to have the highest burden of podoconiosis globally, but the geographical distribution and environmental limits and correlates are yet to be fully investigated. In this paper we use data from a nationwide survey to address these issues.

Methodology

Our analyses are based on data arising from the integrated mapping of podoconiosis and lymphatic filariasis (LF) conducted in 2013, supplemented by data from an earlier mapping of LF in western Ethiopia in 2008–2010. The integrated mapping used woreda (district) health offices’ reports of podoconiosis and LF to guide selection of survey sites. A suite of environmental and climatic data and boosted regression tree (BRT) modelling was used to investigate environmental limits and predict the probability of podoconiosis occurrence.

Principal Findings

Data were available for 141,238 individuals from 1,442 communities in 775 districts from all nine regional states and two city administrations of Ethiopia. In 41.9% of surveyed districts no cases of podoconiosis were identified, with all districts in Affar, Dire Dawa, Somali and Gambella regional states lacking the disease. The disease was most common, with lymphoedema positivity rate exceeding 5%, in the central highlands of Ethiopia, in Amhara, Oromia and Southern Nations, Nationalities and Peoples regional states. BRT modelling indicated that the probability of podoconiosis occurrence increased with increasing altitude, precipitation and silt fraction of soil and decreased with population density and clay content. Based on the BRT model, we estimate that in 2010, 34.9 (95% confidence interval [CI]: 20.2–51.7) million people (i.e. 43.8%; 95% CI: 25.3–64.8% of Ethiopia’s national population) lived in areas environmentally suitable for the occurrence of podoconiosis.

Conclusions

Podoconiosis is more widespread in Ethiopia than previously estimated, but occurs in distinct geographical regions that are tied to identifiable environmental factors. The resultant maps can be used to guide programme planning and implementation and estimate disease burden in Ethiopia. This work provides a framework with which the geographical limits of podoconiosis could be delineated at a continental scale.     

中国侧棘斑蚜属(蚜科,角斑蚜亚科)地理分布格局研究

用GIs技术研究斑蚜科侧棘斑蚜属Tuberculatus在中国的地理分布格局。种类以县级行政单元转换地理坐标与动物地理区划图叠加后产生蚜虫地理分布图。结果显示出这个属主要分布在东北区南部、华北区、华中区、华南区和西南区东部(中国南部和东部)。根据地理分布图及有关统计分析,认为东北区南部—华北区北部和华中区南部一东南部是这个属在中国的分布中心、分化中心和特有中心。同时,利用寄主植物的分布,探讨了中国侧棘斑蚜属的分布与寄主植物分布之间的关系。