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Background: The biological interpretation of large-scale gene expression data is one of the paramount challenges in current bioinformatics. In particular, placing the results in the context of other available functional genomics data, such as existing bio-ontologies, has already provided substantial improvement for detecting and categorizing genes of interest. One common approach is to look for functional annotations that are significantly enriched within a group or cluster of genes, as compared to a reference group. Results: In this work, we suggest the information-theoretic concept of mutual information to investigate the relationship between groups of genes, as given by data-driven clustering, and their respective functional categories. Drawing upon related approaches (Gibbons and Roth, Genome Research 12: 1574-1581, 2002), we seek to quantify to what extent individual attributes are sufficient to characterize a given group or cluster of genes. Conclusion: We show that the mutual information provides a systematic framework to assess the relationship between groups or clusters of genes and their functional annotations in a quantitative way. Within this framework, the mutual information allows us to address and incorporate several important issues, such as the interdependence of functional annotations and combinatorial combinations of attributes. It thus supplements and extends the conventional search for overrepresented attributes within a group or cluster of genes. In particular taking combinations of attributes into account, the mutual information opens the way to uncover specific functional descriptions of a group of genes or clustering result. All datasets and functional annotations used in this study are publicly available. All scripts used in the analysis are provided as additional files.
We report quantum chemical calculations, mostly based on density functional theory, on azobenzene and substituted azobenzenes as neutral molecules or ions, in ground and excited states. Both the cis and trans configurations are computed as well as the activation energies to transform one isomer into the other and the possible reaction paths and reaction surfaces along the torsion and inversion modes. All calculations are done for the isolated species, but results are discussed in light of recent experiments aiming at the switching of surface mounted azobenzenes by scanning tunneling microscopes.
Dynamic service adaptation
(2006)
Change can be observed in our environment and in the technology we build. While changes in the environment happen continuously and implicitly, our technology has to be kept in sync with the changing world around it. Although we can prepare for some of the changes for most of them we cannot. This is especially true for next-generation mobile communication systems that are expected to support the creation of a ubiquitous society where virtually everything is connected and made available within an organic information network. Resources will frequently join or leave the network, new types of media or new combinations of existing types will be used to interact and cooperate, and services will be tailored to preferences and needs of individual customers to better meet their needs. This paper outlines our research in the area of dynamic service adaptation to provide concepts and technologies allowing for such environments. Copyright (C) 2006 John Wiley & Sons, Ltd.
We introduce a method for computing instantaneous-polarization attributes from multicomponent signals. This is an improvement on the standard covariance method (SCM) because it does not depend on the window size used to compute the standard covariance matrix. We overcome the window-size problem by deriving an approximate analytical formula for the cross-energy matrix in which we automatically and adaptively determine the time window. The proposed method uses polarization analysis as applied to multicomponent seismic by waveform separation and filtering.
Seasonal, host sex and age-related variations in helminth egg and coccidian oocyst counts were investigated in a naturally infected wild bushbuck (Tragelaphus scriptus) population in Queen Elizabeth National Park, western Uganda from April 2000 to February 2002. The prevalence and mean intensity quantified as the number of eggs and oocysts per gram of faeces were taken as a measure of parasite burdens. Host sex and age-related differences in prevalence values were not found but the overall prevalence of Eimeria sp. was significantly higher during the rainy season, and peak counts were recorded either during or soon after a peak rainfall. A similar trend was observed for Moniezia spp., although the results were marginally not significant. There were also no significant differences in mean intensity values, relative to host sex, age or season.
[ 1] In this paper, we discuss the origin of superswell volcanism on the basis of representation and analysis of recent gravity and magnetic satellite data with wavelets in spherical geometry. We computed a refined gravity field in the south central Pacific based on the GRACE satellite GGM02S global gravity field and the KMS02 altimetric grid, and a magnetic anomaly field based on CHAMP data. The magnetic anomalies are marked by the magnetic lineation of the seafloor spreading and by a strong anomaly in the Tuamotu region, which we interpret as evidence for crustal thickening. We interpret our gravity field through a continuous wavelet analysis that allows to get a first idea of the internal density distribution. We also compute the continuous wavelet analysis of the bathymetric contribution to discriminate between deep and superficial sources. According to the gravity signature of the different chains as revealed by our analysis, various processes are at the origin of the volcanism in French Polynesia. As evidence, we show a large-scale anomaly over the Society Islands that we interpret as the gravity signature of a deeply anchored mantle plume. The gravity signature of the Cook-Austral chain indicates a complex origin which may involve deep processes. Finally, we discuss the particular location of the Marquesas chain as suggesting that the origin of the volcanism may interfere with secondary convection rolls or may be controlled by lithospheric weakness due to the regional stress field, or else related to the presence of the nearby Tuamotu plateau.
Reliable information on small- and medium-sized enterprises (SMEs) is rare and costly for financial intermediaries. Therefore relationship banking is often considered as the appropriate lending technique. In this paper we offer a theoretical model to analyze relationship banking and the pricing behavior of banks in a Bertrand competition framework with monitoring costs. We show that the lack of reliable information leads to comparable high interest rates even if a long-term relationship between borrower and bank exists. The paper offers a theoretical explanation why SMEs often are faced with borrowing constraints.
Quantification of discrete pressure-temperature domains in deformed chlorite + white mica-bearing metapelites was undertaken on mineral compositions derived by two-dimensional microprobe compositional mapping of selected areas of rock thin sections. In order to achieve compositional information at sufficient analytical precision, spatial resolution and sample coverage within a typical analysis time of 1 day, an optimization of measurement methods was necessary. The method presented here allows collection of raw counts for eight different element concentrations at an analytical precision of similar to 1-2 wt%. X-ray intensity multiplane maps (one map per measured chemical element) are translated into concentration multiplane maps, utilizing selected conventionally measured spot analyses combined with the Castaing approximation for each mineral. As this step requires identification of the different minerals present in the mapped area, a statistical clustering technique to identify different groups of composition was developed, guided by simple petrographic inspection of the thin section, to delineate the important minerals in the mapped area. Finally, the compositions of each pixel are translated into a mineral structural formula thus yielding a new kind of image with a high content of petrological information. The reliability of the mineral composition images was emphasized by carrying out precision tests on the analytical data. The possible use of chemical maps to infer the P-T-deformation history of metamorphic rocks is illustrated with two samples from the Spitzbergen and the Sambagawa blueschist facies belts. In both samples, a strong correlation between structures and chemistry is observed. Qualitative estimates of P-T conditions from the Si-content of mica and chlorite are in good agreement with their location in microstructures that formed at different times. Therefore, the combination of chemical maps with microstructural observations is a very powerful approach to understand both the evolution of complex metamorphic rocks and the control by deformation of mineral reactivity.
Incremental Support Vector Machines (SVM) are instrumental in practical applications of online learning. This work focuses on the design and analysis of efficient incremental SVM learning, with the aim of providing a fast, numerically stable and robust implementation. A detailed analysis of convergence and of algorithmic complexity of incremental SVM learning is carried out. Based on this analysis, a new design of storage and numerical operations is proposed, which speeds up the training of an incremental SVM by a factor of 5 to 20. The performance of the new algorithm is demonstrated in two scenarios: learning with limited resources and active learning. Various applications of the algorithm, such as in drug discovery, online monitoring of industrial devices and and surveillance of network traffic, can be foreseen.
Successful pain treatment in arthropathic lower extremities by acupuncture in haemophilia patients
(2006)
Acupuncture is successfully used in the treatment of degenerative osteoarthritis. The treatment of haemophilic arthropathies can require strong painkillers with severe side-effects. Therefore, a special yet simple acupuncture technique was evaluated in the treatment of these joint problems. Twelve patients with a factor VIII activity < 1% and at least one painful arthropathy in both lower extremities were included in this single-blinded study. The non-treated side served as a control. Treatment was assessed by a visual analogue scale (VAS) and an orthopaedic clinical examination. Only one needle was inserted at the rear fontanelle once per week and in 15 cycles. Ten of 12 patients showed an improvement of their pain perception. The average VAS could be reduced from 6.8 to 5.0. The side not receiving treatment showed a reduction from 4.1 to 4.0. No side-effects were observed. Even though interpretation of our data are limited due to the small patient numbers, significant improvement of the VAS after treatment suggests that acupuncture has a measurable positive effect in pain management for haemophilic arthropathy of the lower extremities.