Genetic algorithm based two-mode clustering of metabolomics data

Metabolomics and other omics tools are generally characterized by large data sets with many variables obtained under different environmental conditions. Clustering methods and more specifically two-mode clustering methods are excellent tools for analyzing this type of data. Two-mode clustering methods allow for analysis of the behavior of subsets of metabolites under different experimental conditions. In addition, the results are easily visualized. In this paper we introduce a two-mode clustering method based on a genetic algorithm that uses a criterion that searches for homogeneous clusters. Furthermore we introduce a cluster stability criterion to validate the clusters and we provide an extended knee plot to select the optimal number of clusters in both experimental and metabolite modes. The genetic algorithm-based two-mode clustering gave biological relevant results when it was applied to two real life metabolomics data sets. It was, for instance, able to identify a catabolic pathway for growth on several of the carbon sources

Bylaag: Natuurwet en waarheid*

Die betekenis van natuurwetenskaplike arbeid lê opgesluit in die „natuurwet” en die „waarheid”. Met die natuurwet beheer die natuurwetenskaplike die natuurkragte en verkry hy 'n insig in die natuur wat hom omring. Die waarheid is vir hom die ooreenkoms tussen die natuurgebeure en die verklarende natuurwetenskaplike teorie

Perceived heading during simulated torsional eye movements

AbstractObserver translation through the environment can be accompanied by rotation of the eye about any axis. For rotation about the vertical axis (horizontal rotation) during translation in the horizontal plane, it is known that the absence of depth in the scene and an extra retinal signal leads to a systematic error in the observer’s perceived direction of heading. This heading error is related in magnitude and direction to the shift of the centre of retinal flow (CF) that occurs because of the rotation. Rotation about any axis that deviates from the heading direction results in a CF shift. So far, however, the effect of rotation about the line of sight (torsion) on perceived heading has not been investigated. We simulated observer translation towards a wall or cloud, while simultaneously simulating eye rotation about the vertical axis, the torsional axis or combinations thereof. We find only small systematic effects of torsion on the set of 2D perceived headings, regardless of the simulated horizontal rotation. In proportion to the CF shift, the systematic errors are significantly smaller for pure torsion than for pure horizontal rotation. In contrast to errors caused by horizontal rotation, the torsional errors are hardly reduced by addition of depth to the scene. We suggest the difference in behaviour reflects the difference in symmetry of the field of view relative to the axis of rotation: the higher symmetry in the case of torsion may allow for a more accurate estimation of the rotational flow. Moreover, we report a new phenomenon. Simulated horizontal rotation during simulated wall approach increases the heading-dependency of errors, causing a larger compression of perceived heading in the horizontal direction than in the vertical direction

The art of creating futures. Practical theology and a strategic research sensitivity for the future

This paper explores a futures perspective for practical theology. Although there are some examples of a future orientation, a systematic futures perspective has not been developed. Building on futures studies (including predictive studies on foresight and design and architecture studies), the authors propose a methodological model for future-sensitive practical theology, accounting for the probable, possible, and preferable. The model results in three modes in which practical theology can employ a future orientation: utopian, prognostic-adaptive, and designing-creative

Genes involved in carotene synthesis and mating in Blakeslea trispora

Mating of Blakeslea trispora and other molds of the order Mucorales requires the interaction of mycelia of opposite sex, (+) and (-), leading to the development of specialized structures and to an enhanced accumulation of beta-carotene. Industry obtains beta-carotene by co-cultivating appropriate strains of Blakeslea (mated cultures). Gene transcription in single and mated cultures was assayed by cDNA-AFLP, a technique to observe the differential expression of subsets of mRNA fragments. Overexpression in mated cultures is about ten times more frequent than underexpression. We obtained and sequenced fragments of 97 candidate genes that appeared to be overexpressed during mating and confirmed four of them by reverse transcription and real-time PCR. Comparisons with gene sequences from other organisms suggest functions in carotene biosynthesis (4 genes), energy metabolism (8), cell wall synthesis (1), transfer of acetyl groups (1), and regulatory processes (10). Sodium acetate inhibited sexual overexpression in about two-thirds of the candidate genes and acted as a signal with broad effects on the metabolism and the morphology of mated cultures. Our work offers new materials for the study of carotene biosynthesis and its regulation and for the improvement of carotene production with Mucorales

Occlusion-related lateral connections stabilize kinetic depth stimuli through perceptual coupling

Local sensory information is often ambiguous forcing the brain to integrate spatiotemporally separated information for stable conscious perception. Lateral connections between clusters of similarly tuned neurons in the visual cortex are a potential neural substrate for the coupling of spatially separated visual information. Ecological optics suggests that perceptual coupling of visual information is particularly beneficial in occlusion situations. Here we present a novel neural network model and a series of human psychophysical experiments that can together explain the perceptual coupling of kinetic depth stimuli with activity-driven lateral information sharing in the far depth plane. Our most striking finding is the perceptual coupling of an ambiguous kinetic depth cylinder with a coaxially presented and disparity defined cylinder backside, while a similar frontside fails to evoke coupling. Altogether, our findings are consistent with the idea that clusters of similarly tuned far depth neurons share spatially separated motion information in order to resolve local perceptual ambiguities. The classification of far depth in the facilitation mechanism results from a combination of absolute and relative depth that suggests a functional role of these lateral connections in the perception of partially occluded objects

BMSSM Implications for Cosmology

The addition of non-renormalizable terms involving the Higgs fields to the MSSM (BMSSM) ameliorates the little hierarchy problem of the MSSM. We analyze in detail the two main cosmological issues affected by the BMSSM: dark matter and baryogenesis. The regions for which the relic abundance of the LSP is consistent with WMAP and collider constraints are identified, showing that the bulk region and other previously excluded regions are now permitted. Requiring vacuum stability limits the allowed regions. Based on a two-loop finite temperature effective potential analysis, we show that the electroweak phase transition can be sufficiently first order in regions that for the MSSM are incompatible with the LEP Higgs mass bound, including parameter values of \tan\beta \lsim 5, m_{\tilde{t}_{1}} > m_t, m_Q << TeV.Comment: 28 pages, 4 figures. References adde

Statistical mechanics of random two-player games

Using methods from the statistical mechanics of disordered systems we analyze the properties of bimatrix games with random payoffs in the limit where the number of pure strategies of each player tends to infinity. We analytically calculate quantities such as the number of equilibrium points, the expected payoff, and the fraction of strategies played with non-zero probability as a function of the correlation between the payoff matrices of both players and compare the results with numerical simulations.Comment: 16 pages, 6 figures, for further information see http://itp.nat.uni-magdeburg.de/~jberg/games.htm

’N narratiewe teologiese verkenning van negatiewe koronêre vatomleidingsoperasieuitkomste: ’n chirurgiese hermeneutiek

Negative outcomes of coronary bypass operations not only have an important impact on the patient and family, but also have an influence on the cardiac surgeon on many levels. Within a specific surgical context and from a tradition of faith, interwoven narratives present the possibility of an interdisciplinary conversation between medical science and theology. By following an auto-ethnographic approach, an invitation is offered to participate in sharing the surgeon’s database as a new hermeneutic text. Fellow cardiac surgeons on a national level are involved by way of a Delphi research model, providing for a collective tracing of God’s involvement in surgical outcomes. In a process of a reinterpretation of negative surgical outcomes, Henri Nouwen’s three poles of a spiritual movement can lead to spiritual transformation. Bearing physiological barriers and lifestyles in mind, as well as God’s involvement, the patient and surgeon can in a new manner reflect on possible negative outcomes following operative procedures