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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.
Plastidial phosphorylase is required for normal starch synthesis in Chlamydomonas reinhardtii
(2006)
Among the three distinct starch phosphorylase activities detected in Chlamydomonas reinhardtii, two distinct plastidial enzymes (PhoA and PhoB) are documented while a single extraplastidial form (PhoC) displays a higher affinity for glycogen as in vascular plants. The two plastidial phosphorylases are shown to function as homodimers containing two 91-kDa (PhoA) subunits and two 110-kDa (PhoB) subunits. Both lack the typical 80-amino-acid insertion found in the higher plant plastidial forms. PhoB is exquisitely sensitive to inhibition by ADP-glucose and has a low affinity for malto-oligosaccharides. PhoA is more similar to the higher plant plastidial phosphorylases: it is moderately sensitive to ADP-glucose inhibition and has a high affinity for unbranched malto-oligosaccharides. Molecular analysis establishes that STA4 encodes PhoB. Chlamydomonas reinhardtii strains carrying mutations at the STA4 locus display a significant decrease in amounts of starch during storage that correlates with the accumulation of abnormally shaped granules containing a modified amylopectin structure and a high amylose content. The wild-type phenotype could be rescued by reintroduction of the cloned wild-type genomic DNA, thereby demonstrating the involvement of phosphorylase in storage starch synthesis.
Experimental results show that the polymerization of pyrrole in the presence of beta-naphthalenesulfonic acid and different fluorosurfactants like perfluorooctanesulfonic acid, perfluorooctyldiethanolamide, and ammonium perfluorooctanoate leads to polypyrrole with special morphologies, such as rings or disks and rectangular frames or plates. The formation of these unusually shaped particles of polymer dispersions is explained by the chemical and colloidal peculiarities of the oxidative pyrrole polymerization with ammonium peroxodisulfate in aqueous medium.
Sexual dimorphism is expressed as median of the female values in percent of the median of the male values, of 4 length measurements, 3 circumferences, and 5 measurements of corpulence respectively fat. Data were obtained from a cross-sectional sample of more than 41.000 German subjects, aged from birth to age 62. The pattern of sexual dimorphism is similar in the length measurements. Girls are shorter at birth, but they increase in length at higher rates than boys and even temporarily overgrow the boys up to age 12. Thereafter, males show an obvious growth advantage leading to some 6 to 9% more length in adult males. In contrast, female circumferences are always smaller, from birth to senescence. Though, the differences between the sexes are low in circumferences, up to age 13, sexual dimorphism increases to 17% in the thoracic circumference at adulthood. Sexual dimorphism in weight and BMI is comparably with that in length measurements while subcutaneous fat and total body fat content are always higher in females. The results highlight that sexual dimorphism develops at different pace in the various components of the body and that it associates with a sex specific growth tempo.
The efficient time integration of the dynamic core equations for numerical weather prediction (NWP) remains a key challenge. One of the most popular methods is currently provided by implementations of the semi-implicit semi-Lagrangian (SISL) method, originally proposed by Robert (J. Meteorol. Soc. Jpn., 1982). Practical implementations of the SISL method are, however, not without certain shortcomings with regard to accuracy, conservation properties and stability. Based on recent work by Gottwald, Frank and Reich (LNCSE, Springer, 2002), Frank, Reich, Staniforth, White and Wood (Atm. Sci. Lett., 2005) and Wood, Staniforth and Reich (Atm. Sci. Lett., 2006) we propose an alternative semi-Lagrangian implementation based on a set of regularized equations and the popular Stormer-Verlet time stepping method in the context of the shallow-water equations (SWEs). Ultimately, the goal is to develop practical implementations for the 3D Euler equations that overcome some or all shortcomings of current SISL implementations.
Glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD) are required for normal starch metabolism. We analysed starch phosphorylation in Arabidopsis wildtype plants and mutants lacking either GWD or PWD using P-31 NMR. Phosphorylation at both C6- and C3-positions of glucose moieties in starch was drastically decreased in GWD-deficient mutants. In starch from PWD-deficient plants C3-bound phosphate was reduced to levels close to the detection limit. The latter result contrasts with previous reports according to which GWD phosphorylates both C6- and C3-positions. In these studies, phosphorylation had been analysed by HPLC of acid-hydrolysed glucans. We now show that maltose-6-phosphate, a product of incomplete starch hydrolysis, co-eluted with glucose-3-phosphate under the chromatographic conditions applied. Re-examination of the specificity of the dikinases using an improved method demonstrates that C6- and C3-phosphorylation is selectively catalysed by GWD and PWD, respectively.
The AtNFXL1 gene encodes a NF-X1 type zinc finger protein required for growth under salt stress
(2006)
The human NF-X1 protein and homologous proteins in eukaryotes represent a class of transcription factors which are characterised. by NF-X1 type zinc finger motifs. The Arabidopsis genome encodes two NF-X1 homologs, which we termed AtNFXL1 and AtNFXL2. Growth and survival was impaired in atnfxl1 knock-out mutants and AtNFXL1-antisense plants under salt stress in comparison to wild-type plants. In contrast, 35S: :AtNFXL1 plants showed higher survival rates. The AtNFXL2 protein potentially plays an antagonistic role. The Arabidopsis NF-X1 type zinc finger proteins likely are part of regulatory mechanisms, which protect major processes such as photosynthesis.
The fabrication of compartmented micellar systems is an exciting new area of research in the field of polymer self-assembly. Multicompartment micelles composed of a water-soluble shell and a segregated hydrophobic core can be obtained via direct aqueous self-assembly of preformed polymeric amphiphiles possessing one hydrophilic segment and two incompatible hydrophobic segments (e.g. hydrocarbon and fluorocarbon blocks). Such macromolecular building-blocks were prepared in the present work principally via reversible addition-fragmentation transfer polymerization (RAFT). Polysoaps or triblock macrosurfactants can be synthesized in high yields by RAFT under relatively straightforward experimental conditions.
[1] We document late Pleistocene - Holocene aggradation and incision processes at the mountain front of the Qilian Shan, an active intracontinental fold-and-thrust belt accommodating a significant portion of the India-Asia convergence. The Shiyou River cuts through a NNE vergent fault propagation fold with Miocene red beds in the core and Pliocene - Quaternary growth strata on the northern forelimb. South of the anticline, Miocene strata dip 20 degrees SSW, suggesting a similar orientation for the basal decollement. After aggradation of an similar to 150-m-thick, late Pleistocene valley fill, the Shiyou River formed three terraces. The highest terrace, located 170 m above the river, constitutes the top of the fill. The other terraces are fill cut terraces: their treads are located 130 - 105 m and 37 m above the river, respectively. The 10 Be exposure dating of the terraces suggests that river incision accelerated from 0.8 +/- 0.2 mm yr(-1) to similar to 10 mm yr(-1) at 10 - 15 kyr. We interpret fast Holocene river incision as largely unrelated to tectonic forcing. The late Pleistocene incision rate of 0.8 +/- 0.2 mm yr(-1) places an upper limit of 2.2 +/- 0.5 mm yr(-1) on the horizontal shortening rate, assuming that incision is solely caused by rock uplift above a decollement dipping 20 degrees. However, the actual shortening rate may lie between similar to 2.2 mm yr(-1) and zero because deformation of the terraces and the valley fill cannot be unequivocally demonstrated. Our estimate is consistent with the bulk shortening rate of similar to 5 - 10 mm yr(-1) across several faults in NE Tibet derived from neotectonic and GPS data, although in case of the Shiyou River, Holocene deformation is barely discernible owing to intense climate-induced river incision.
Many semi-arid regions are characterised by water scarcity and vulnerability of natural resources, pronounced climatic variability and social stress. Integrated studies including climatotogy, hydrology, and socio-econornic studies are required both for analysing the dynamic natural conditions and to assess possible strategies to make semi-arid regions Less vulnerable to the present and changing climate. The model introduced here dynamically describes the retationships between climate forcing, water availability, agriculture and selected societal processes. The model has been tailored to simulate the rather complex situation in the semi-and north-eastern Brazil in a quantitative manner including the sensitivity to external forcing, such as climate change. The selected results presented show the general functioning of the integrated model, with a primary focus on climate change impacts. It becomes evident that due to Large differences in regional climate scenarios, it is still impossible to give quantitative values for the most probable development, e.g., to assign probabilities to the simulated results. However, it becomes clear that water is a very crucial factor, and that an efficient and ecologically sound water management is a key question for the further development of that semi-arid region. The simulation results show that, independent of the differences in climate change scenarios, rain-fed farming is more vulnerable to drought impacts compared to irrigated farming. However, the capacity of irrigation and other water infrastructure systems to enhance resilience in respect to climatic fluctuations is significantly constrained given a significant negative precipitation trend. (c) 2005 Elsevier B.V. All rights reserved.