Day: August 6, 2010

New Map Shows Estimates of the Global Population at Risk of Plasmodium Vivax Malaria

/ Matt Artz / 1 Comment

A new evidence-based global distribution map of Plasmodium vivax malaria, published August 3 in the open-access journal PLoS Neglected Tropical Diseases, is used to estimate that 2.85 billion people lived at risk of infection with this parasite in 2009. The map, created as part of the Malaria Atlas Project (MAP), a multinational research collaboration funded mainly by the Wellcome Trust, reviews a host of information that challenges the dogma that P. vivax transmission is absent through large swathes of Africa and uses novel methods – including new global maps of the protective Duffy negativity blood condition – to estimate global populations at risk.

The study concludes that of the almost 3 billion people exposed to some risk of P. vivax transmission in 2009, 91% of them live in Central and South East Asia. Importantly, more than half of those exposed to this risk live in areas where P. vivax malaria transmission is extremely low or unstable and where prospects of sustained control and elimination are relatively good.

The authors used the most recent obtainable P. vivax case-reporting data for all malaria-endemic countries in efforts to classify risk into three classes: malaria free, unstable, and stable. Risk areas were further refined using temperature and aridity data based upon their relationship with parasite and vector bionomics. Medical intelligence was used to modify risk in specific areas where transmission was reported as absent (e.g., large urban areas and malaria-free islands). The human population at risk under each level of transmission was then derived by combining the categorical risk map with a high-resolution population surface adjusted to 2009 and a global map of Duffy negativity prevalence. Duffy negativity is the absence of the Duffy blood-group antigen in red blood cells, which translates into partial protection against infection with P. vivax. A high Duffy negativity prevalence in a population indicates increased protection against P. vivax infection, and vice versa.

“This study represents the first step in our efforts to provide the malaria control and research community with an evidence-based cartography of P. vivax malaria,” says co-author Dr. Simon Hay of the University of Oxford. “We can now focus on trying to model the endemicity of the disease to provide more detailed global burden estimates, although this is complicated by the unusual biology of P. vivax“.

Co-author Dr Carlos Guerra adds: “New evidence shows that P. vivax malaria is not as benign as was thought, and yet, as our study shows, remains the most widespread form of human malaria. Understanding where transmission of this parasite occurs at the global scale is fundamental in planning strategies for the control of this debilitating, and often lethal, disease”.

Further information about the Malaria Atlas Project can be found at www.map.ox.ac.uk.

Guerra CA, Howes RE, Patil AP, Gething PW, Van Boeckel TP, et al. (2010) The International Limits and Population at Risk of Plasmodium vivax Transmission in 2009. PLoS Negl Trop Dis 4(8): e774.

[Source: University of Oxford press release]

AGU Informatics Session on Encouraging and Enabling Transparency in Science Data

/ Matt Artz

2010 American Geophysical Union (AGU) Fall Meeting
13–17 December
San Francisco, California, USA

“A number of events and publications have highlighted the need for a high degree of transparency and best practices in the publication, management, provenance tracking, traceability, identification, and citability of science data, and particularly for Earth Science data. Motivation to publish data also comes from publisher and funding agency mandates to make data accessible and a desire to give greater credit for the sharing of data. This session is for the tools, approaches, and cultural changes to increase the transparency of scientific work, improve the analysis of the impact of data sharing, and provide credit for researchers and institutions openly sharing data. This session is accompanied by an overview Union session, U17.”

Exploring Place through User-generated Content: Using Flickr to Describe City Cores

/ Matt Artz / 1 Comment

Journal of Spatial Information Science, Number 1 (2010), pp. 21-48

Livia Hollenstein and Ross Purves

“Terms used to describe city centers, such as Downtown, are key concepts in everyday or vernacular language. Here, we explore such language by harvesting georeferenced and tagged metadata associated with 8 million Flickr images and thus consider how large numbers of people name city core areas. The nature of errors and imprecision in tagging and georeferencing are quantified, and automatically generated precision measures appear to mirror errors in the positioning of images. Users seek to ascribe appropriate semantics to images, though bulk-uploading and bulk-tagging may introduce bias. Between 0.5–2% of tags associated with georeferenced images analyzed describe city core areas generically, while 70% of all georeferenced images analyzed include specific place name tags, with place names at the granularity of city names being by far the most common. Using Flickr metadata, it is possible not only to describe the use of the term Downtown across the USA, but also to explore the borders of city center neighborhoods at the level of individual cities, whilst accounting for bias by the use of tag profiles.”

Post-harvest Mortality in Selection-managed Northern Hardwoods: A Spatial Analysis of Edge Effects

/ Matt Artz

95th Ecological Society of America (ESA) Annual Meeting, Pittsburgh, PA, 01-06 August 2010

Michael M. Fuller, Fraser H. Smith, and Sean C. Thomas

“Background/Question/Methods: Selection management, which maintains an uneven-aged stand structure and high canopy cover, has been promoted as an ecologically sustainable form of forest management. Although retention harvesting may immediately preserve integral forest structural characteristics, adequate evaluation of stand responses will determine the success or failure of such treatments. In previous work, we quantified a temporal spike in stem mortality following retention harvest. While the mechanisms underlying this increase in post-harvest mortality (PHM) are generally understood, the patterns of mortality are unclear, particularly in operational stands. Here we analyzed the influence of the cut block edge on the rate and spatial pattern of PHM for four different mortality classes in Yukon boreal forest. The different mortality classes relate closely to specific mechanisms by which stems die, such as by wind throw and fungal attack. Using 20m radius sample plots set along the forest edge of retention plots, we computed the frequency and spatial-dependency of mortality for each class.

“Results/Conclusions: Distance from the edge of the cut block influenced the rate of mortality for stems located within intact forest along the boundary of retention plots. The rate of mortality differed among the four mortality classes, suggesting that the mechanisms influencing PHM are spatially heterogeneous. Our results indicate that efforts to mitigate the negative impacts of selection management can be improved by recognizing how the major drivers of PHM change with the spatial proximity, and possibly the shape characteristics, of the cut block edge.”

New Chief for USGS National Climate Change and Wildlife Science Center

/ Matt Artz

Doug Beard has been selected as the chief of the USGS National Climate Change and Wildlife Science Center.

The NCCWSC is helping understand climate change impacts on fish and wildlife and develop tools that resource managers can use to protect these species and their habitats.

“Earth’s climate is expected to have significant impacts on our nation’s fish and wildlife now and in the future,” said Beard. “The USGS NCCSWS is providing sound science on how the climate may change and how landscapes and habitats will respond, helping managers develop effective strategies to protect species survival.”

Beard had already been serving as the interim director of the USGS NCCWSC since September 2009. Previously, he was the USGS program coordinator for fisheries and aquatic and endangered resources. He first joined the USGS in 2003, working as a program manager with the National Biological Information Infrastructure. Before coming to the USGS, he held fishery management positions in Wisconsin and Minnesota Departments of Natural Resources. He received a bachelor’s in biology from the University of Wisconsin – Eau Claire, a master’s in fish and wildlife from Pennsylvania State University, and a doctorate in zoology from the University of Wisconsin – Madison.

Beard will also oversee the establishment and program direction of the Department of the Interior’s eight regional Climate Science Centers. These CSCs will provide scientific information, tools and techniques needed to manage land, water, wildlife and cultural resources in the face of climate change. The NCCWSC and other USGS scientific programs will work closely with these CSCs.

The USGS and the DOI CSCs will work with a network of Landscape Conservation Cooperatives in which federal, state, tribal and other managers and scientists will develop conservation, adaptation and mitigation strategies for dealing with the impacts of climate change.

The NCCWSC was established by Congress in 2008. Projects currently underway include studies of alterations in Florida’s ecosystems, potential impacts on Great Lakes’ fish, sea-level rise impacts on San Francisco Bay marshes, and the effects of melting glaciers on Alaska’s freshwater coastal systems.

Get more information about the USGS NCCWSC, and learn more about the DOI CSCs.

[Source: USGS press release]

Spatial Cluster Analysis of Early Stage Breast Cancer: A Method for Public Health Practice using Cancer Registry Data

/ Matt Artz

Cancer Causes & Control, Volume 20, Issue 7, September 2009

J. Meliker, G. Jacquez, P. Goovaerts, G. Copeland, and M. Yassine

“Cancer registries are increasingly mapping residences of patients at time of diagnosis, however, an accepted protocol for spatial analysis of these data is lacking. We undertook a public health practice-research partnership to develop a strategy for detecting spatial clusters of early stage breast cancer using registry data. Spatial patterns of early stage breast cancer throughout Michigan were analyzed comparing several scales of spatial support, and different clustering algorithms. Analyses relying on point data identified spatial clusters not detected using data aggregated into census block groups, census tracts, or legislative districts. Further, using point data, Cuzick-Edwards’ nearest neighbor test identified clusters not detected by the SaTScan spatial scan statistic. Regression and simulation analyses lent credibility to these findings. In these cluster analyses of early stage breast cancer in Michigan, spatial analyses of point data are more sensitive than analyses relying on data aggregated into polygons, and the Cuzick-Edwards’ test is more sensitive than the SaTScan spatial scan statistic, with acceptable Type I error. Cuzick-Edwards’ test also enables presentation of results in a manner easily communicated to public health practitioners. The approach outlined here should help cancer registries conduct and communicate results of geographic analyses. OBJECTIVES: Cancer registries are increasingly mapping residences of patients at time of diagnosis, however, an accepted protocol for spatial analysis of these data is lacking. We undertook a public health practice-research partnership to develop a strategy for detecting spatial clusters of early stage breast cancer using registry data. METHODS: Spatial patterns of early stage breast cancer throughout Michigan were analyzed comparing several scales of spatial support, and different clustering algorithms. RESULTS: Analyses relying on point data identified spatial clusters not detected using data aggregated into census block groups, census tracts, or legislative districts. Further, using point data, Cuzick-Edwards’ nearest neighbor test identified clusters not detected by the SaTScan spatial scan statistic. Regression and simulation analyses lent credibility to these findings. CONCLUSIONS: In these cluster analyses of early stage breast cancer in Michigan, spatial analyses of point data are more sensitive than analyses relying on data aggregated into polygons, and the Cuzick-Edwards’ test is more sensitive than the SaTScan spatial scan statistic, with acceptable Type I error. Cuzick-Edwards’ test also enables presentation of results in a manner easily communicated to public health practitioners. The approach outlined here should help cancer registries conduct and communicate results of geographic analyses.”

Metadata Requirements Analysis for the Emerging Sensor Web

/ Matt Artz

International Journal of Digital Earth, Volume 2, Issue S1 2009 , pages 3 – 17

Liping Dia, Karen L. Moeb, and Genong (Eugene) Yua

“The Sensor Web has emerged from Earth Science research with the development of Web technology, to achieve process automation, sensor interoperation, and service synergy. These promises require the discovery of the right sensor at the right time and the right location with the right quality. Metadata, for sensor, platform, and data, are crucial for achieving such goals. However, analysis and practical use of these metadata reveals that the metadata and their associations are not applicable or suitable for the Sensor Web. The shortfalls are (1) the non-standard metadata expression language; (2) the missing link between sensor and domain knowledge; (3) the insufficiency in the information for geographic locating and sensor tasking; and (4) the enhanced requirements on the quality, security, and ownership of both sensors and their sensed data. This paper reviews the current standards that have metadata components for the sensor and its platform, especially those from ISO TC211, Open Geospatial Consortium Inc., and The National Aeronautics and Space Administration Global Change Master Directory . A recommendation on metadata that meets the requirement of cross-mission sensor discovery in a pervasive Web environment is derived from them. The recommendation addresses issues on language formalization, sensor geolocation, semantics, quality, and accessibility. Roles of the emerging semantic Web technology for enabling robust discovery of sensor are discussed.”