129,342 research outputs found
Trace element contamination in the arms of the Danube Delta (Romania/Ukraine): Current state of knowledge and future needs
This paper provides the first critical synopsis of contamination by selected trace elements in the whole
Danube Delta (Romania/Ukraine) to: identify general patterns of contamination by trace elements across
the Delta, provide recommendations to refine existing monitoring networks and discuss the potential
toxicity of trace elements in the whole Delta. Sediment samples were collected between 2004 and 2007
in the three main branches of the Delta (Chilia, Sulina and Sfantu Gheorghe) and in the secondary delta of
the Chilia branch. Samples were analyzed for trace elements (Cd, Co, Cr, Cu, Ni, Pb, V, and Zn) and TiO2,
Fe2O3, MnO, CaCO3 and total organic carbon. Cluster analysis (CA) and Principal Component Analysis
(PCA) showed that levels of Cd, Cu, Pb, and Zn were influenced by anthropogenic activities. At the
opposite, concentrations of Cr and Ni largely originated from the weathering of rocks located in the
Romanian part of the Danube catchment and naturally rich in these elements. Data analysis using Self-
Organizing Maps confirmed the conclusions of CA/PCA and further detected that the contamination
tended to be higher in the Chilia and Sulina arms than in the Sfantu Gheorghe arm. The potential
ecological risks due to trace element contamination in the Danube Delta could be identified as moderate
and localized, provided that the presence of the natural sources of Cr and Ni was properly considered.
The available results suggest that monitoring sediment quality at the mouths of Sulina and Sfantu
Gheorghe arms is probably enough to get a picture of the sediment quality along their entire lengths.
However, a larger network of monitoring points is necessary in the Chilia and secondary Chilia delta to
account for the presence of local point sources and for the more complex hydrodynamic of this part of
the Danube Delta
Expression cartography of human tissues using self organizing maps
Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.
Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion, exocrine, epithelium, sexual reproduction, muscle, immune system and nervous tissues). SOM mapping reduces the dimension of expression data from ten thousands of genes to a few thousands of metagenes where each metagene acts as representative of a minicluster of co-regulated single genes. Tissue-specific and common properties shared between groups of tissues emerge as a handful of localized spots in the tissue maps collecting groups of co-regulated and co-expressed metagenes. The functional context of the spots was discovered using overrepresentation analysis with respect to pre-defined gene sets of known functional impact. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. Analysis techniques normally used at the gene-level such as two-way hierarchical clustering provide a better signal-to-noise ratio and a better representativeness of the method if applied to the metagenes. Metagene-based clustering analyses aggregate the tissues into essentially three clusters containing nervous, immune system and the remaining tissues. 
Conclusions: The global view on the behavior of a few well-defined modules of correlated and differentially expressed genes is more intuitive and more informative than the separate discovery of the expression levels of hundreds or thousands of individual genes. The metagene approach is less sensitive to a priori selection of genes. It can detect a coordinated expression pattern whose components would not pass single-gene significance thresholds and it is able to extract context-dependent patterns of gene expression in complex data sets.

Magnification Control in Winner Relaxing Neural Gas
An important goal in neural map learning, which can conveniently be
accomplished by magnification control, is to achieve information optimal coding
in the sense of information theory. In the present contribution we consider the
winner relaxing approach for the neural gas network. Originally, winner
relaxing learning is a slight modification of the self-organizing map learning
rule that allows for adjustment of the magnification behavior by an a priori
chosen control parameter. We transfer this approach to the neural gas
algorithm. The magnification exponent can be calculated analytically for
arbitrary dimension from a continuum theory, and the entropy of the resulting
map is studied numerically conf irming the theoretical prediction. The
influence of a diagonal term, which can be added without impacting the
magnification, is studied numerically. This approach to maps of maximal mutual
information is interesting for applications as the winner relaxing term only
adds computational cost of same order and is easy to implement. In particular,
it is not necessary to estimate the generally unknown data probability density
as in other magnification control approaches.Comment: 14pages, 2 figure
Expression cartography of human tissues using self organizing maps
Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.
Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion, exocrine, epithelium, sexual reproduction, muscle, immune system and nervous tissues). SOM mapping reduces the dimension of expression data from ten thousands of genes to a few thousands of metagenes where each metagene acts as representative of a minicluster of co-regulated single genes. Tissue-specific and common properties shared between groups of tissues emerge as a handful of localized spots in the tissue maps collecting groups of co-regulated and co-expressed metagenes. The functional context of the spots was discovered using overrepresentation analysis with respect to pre-defined gene sets of known functional impact. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. Analysis techniques normally used at the gene-level such as two-way hierarchical clustering provide a better signal-to-noise ratio and a better representativeness of the method if applied to the metagenes. Metagene-based clustering analyses aggregate the tissues into essentially three clusters containing nervous, immune system and the remaining tissues. 
Conclusions: The global view on the behavior of a few well-defined modules of correlated and differentially expressed genes is more intuitive and more informative than the separate discovery of the expression levels of hundreds or thousands of individual genes. The metagene approach is less sensitive to a priori selection of genes. It can detect a coordinated expression pattern whose components would not pass single-gene significance thresholds and it is able to extract context-dependent patterns of gene expression in complex data sets.

Seven properties of self-organization in the human brain
The principle of self-organization has acquired a fundamental significance in the newly emerging field of computational philosophy. Self-organizing systems have been described in various domains in science and philosophy including physics, neuroscience, biology and medicine, ecology, and sociology. While system architecture and their general purpose may depend on domain-specific concepts and definitions, there are (at least) seven key properties of self-organization clearly identified in brain systems: 1) modular connectivity, 2) unsupervised learning, 3) adaptive ability, 4) functional resiliency, 5) functional plasticity, 6) from-local-to-global functional organization, and 7) dynamic system growth. These are defined here in the light of insight from neurobiology, cognitive neuroscience and Adaptive Resonance Theory (ART), and physics to show that self-organization achieves stability and functional plasticity while minimizing structural system complexity. A specific example informed by empirical research is discussed to illustrate how modularity, adaptive learning, and dynamic network growth enable stable yet plastic somatosensory representation for human grip force control. Implications for the design of âstrongâ artificial intelligence in robotics are brought forward
Machine Learning in Wireless Sensor Networks: Algorithms, Strategies, and Applications
Wireless sensor networks monitor dynamic environments that change rapidly
over time. This dynamic behavior is either caused by external factors or
initiated by the system designers themselves. To adapt to such conditions,
sensor networks often adopt machine learning techniques to eliminate the need
for unnecessary redesign. Machine learning also inspires many practical
solutions that maximize resource utilization and prolong the lifespan of the
network. In this paper, we present an extensive literature review over the
period 2002-2013 of machine learning methods that were used to address common
issues in wireless sensor networks (WSNs). The advantages and disadvantages of
each proposed algorithm are evaluated against the corresponding problem. We
also provide a comparative guide to aid WSN designers in developing suitable
machine learning solutions for their specific application challenges.Comment: Accepted for publication in IEEE Communications Surveys and Tutorial
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