Alien Registration- Letovsky, Ethel (Caribou, Aroostook County)

https://digitalmaine.com/alien_docs/26136/thumbnail.jp

Predicting protein functions with message passing algorithms

Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most relevant issues has recently become that of correctly and reliably predicting the functions of observed but still functionally undetermined proteins starting from information coming from the network of co-observed proteins of known functions. Method: The method proposed in this article is based on a message passing algorithm known as Belief Propagation, which takes as input the network of proteins physical interactions and a catalog of known proteins functions, and returns the probabilities for each unclassified protein of having one chosen function. The implementation of the algorithm allows for fast on-line analysis, and can be easily generalized to more complex graph topologies taking into account hyper-graphs, {\em i.e.} complexes of more than two interacting proteins.Comment: 12 pages, 9 eps figures, 1 additional html tabl

Environmental Protection and Economic Development: The Case of the Huaihe River Basin Cleanup Plan

The case examines efforts by the Chinese government and local authorities to restore the Huiahe River, a 1,000 kilometer waterway which runs through four provinces in eastern China. The river basin, covering an area of some 270,000 square kilometers, is home to almost 150 million people and represents one of the most important areas of agricultural output in China. As a result of rapid economic development, the river has, over the past twenty years, become seriously polluted. This has had dire consequences for industries that depend on the river, notably agriculture and fishing. As well, the limited groundwater supplies in eastern China have meant that surface water has always been an important source of supply for residential and industrial uses. The pollution of the Huaihe has therefore had serious public health consequences. In mid-1995, the Chinese government formally adopted an ambitious plan to restore the water quality in the river. The case is based on material gathered from secondary sources, supplemented by interviews conducted with government officials and company managers in Beijing and Anhui province in China. The case begins with an overview of the impact of economic growth on the Chinese environment, and the steps which China has taken to address its growing environmental challenges. The case then focuses on the plan as proposed by the Chinese Research Academy of Environmental Sciences (CRAES). The case goes on to describe some of the early implementation measures taken as part of the plan, in particular the forced closure of hundreds of small factories that have sprung up along the banks of the river. The case outlines the various stakeholders affected by the plan and its ultimate success or failure. These include local residents and businesses, various Chinese government ministries, multilateral lending agencies and international suppliers of anti-pollution technologies. The ultimate success of the plan is, at the time of this writing, not known. Future issues and questions that will affect the plan's success are then described. These include resistance by some elements of the Chinese government concerned about foreign debts incurred to finance the cleanup plan; local officials who may not wish to sacrifice short-term economic growth for environmental protection; and businesses concerned about the financial burden of having to install new clean technologies.http://deepblue.lib.umich.edu/bitstream/2027.42/39536/3/wp147.pd

CAEP 2015 Academic Symposium: Leadership within the emergency medicine academic community and beyond

OBJECTIVES: A panel of emergency medicine (EM) leaders endeavoured to define the key elements of leadership and its models, as well as to formulate consensus recommendations to build and strengthen academic leadership in the Canadian EM community in the areas of mentorship, education, and resources

Environmental Protection and Economic Development: The Case of the Huaihe River Basin Cleanup Plan

The case examines efforts by the Chinese government and local authorities to restore the Huiahe River, a 1,000 kilometer waterway which runs through four provinces in eastern China. The river basin, covering an area of some 270,000 square kilometers, is home to almost 150 million people and represents one of the most important areas of agricultural output in China. As a result of rapid economic development, the river has, over the past twenty years, become seriously polluted. This has had dire consequences for industries that depend on the river, notably agriculture and fishing. As well, the limited groundwater supplies in eastern China have meant that surface water has always been an important source of supply for residential and industrial uses. The pollution of the Huaihe has therefore had serious public health consequences. In mid-1995, the Chinese government formally adopted an ambitious plan to restore the water quality in the river. The case is based on material gathered from secondary sources, supplemented by interviews conducted with government officials and company managers in Beijing and Anhui province in China. The case begins with an overview of the impact of economic growth on the Chinese environment, and the steps which China has taken to address its growing environmental challenges. The case then focuses on the plan as proposed by the Chinese Research Academy of Environmental Sciences (CRAES). The case goes on to describe some of the early implementation measures taken as part of the plan, in particular the forced closure of hundreds of small factories that have sprung up along the banks of the river. The case outlines the various stakeholders affected by the plan and its ultimate success or failure. These include local residents and businesses, various Chinese government ministries, multilateral lending agencies and international suppliers of anti-pollution technologies. The ultimate success of the plan is, at the time of this writing, not known. Future issues and questions that will affect the plan's success are then described. These include resistance by some elements of the Chinese government concerned about foreign debts incurred to finance the cleanup plan; local officials who may not wish to sacrifice short-term economic growth for environmental protection; and businesses concerned about the financial burden of having to install new clean technologies.

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources

Expert Programming Knowledge: a Schema-Based Approach

The topic of this chapter is the role of expert programming knowledge in the understanding activity. In the "schema-based approach", the role of semantic structures is emphasized whereas, in the "control-flow approach", the role of syntactic structures is emphasized. Data which support schema-based models of understanding are presented. Data which are more consistent with the "control-flow approach" allow to discuss the limits of the former kind of models

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources

Transcription factor Sp1 is essential for early embryonic development but dispensable for cell growth and differentiation.

Transcription factor Sp1 has been implicated in the expression of many genes. Moreover, it has been suggested that Sp1 is linked to the maintenance of methylation-free CpG islands, the cell cycle, and the formation of active chromatin structures. We have inactivated the mouse Sp1 gene. Sp1-/- embryos are retarded in development, show a broad range of abnormalities, and die around day 11 of gestation. In Sp1-/- embryos, the expression of many putative target genes, including cell cycle-regulated genes, is not affected, CpG islands remain methylation free, and active chromatin is formed at the globin loci. However, the expression of the methyl-CpG-binding protein MeCP2 is greatly reduced in Sp1-/- embryos. MeCP2 is thought to be required for the maintenance of differentiated cells. We suggest that Sp1 is an important regulator of this process