1,949 research outputs found
Mining Biclusters of Similar Values with Triadic Concept Analysis
Biclustering numerical data became a popular data-mining task in the
beginning of 2000's, especially for analysing gene expression data. A bicluster
reflects a strong association between a subset of objects and a subset of
attributes in a numerical object/attribute data-table. So called biclusters of
similar values can be thought as maximal sub-tables with close values. Only few
methods address a complete, correct and non redundant enumeration of such
patterns, which is a well-known intractable problem, while no formal framework
exists. In this paper, we introduce important links between biclustering and
formal concept analysis. More specifically, we originally show that Triadic
Concept Analysis (TCA), provides a nice mathematical framework for
biclustering. Interestingly, existing algorithms of TCA, that usually apply on
binary data, can be used (directly or with slight modifications) after a
preprocessing step for extracting maximal biclusters of similar values.Comment: Concept Lattices and their Applications (CLA) (2011
Konzeption und Entwicklung eines Generators ereignisbasierter Patientendaten fĂĽr ein virtuelles Gesundheitssystem
Das deutsche Gesundheitswesen ist ein dichtes Netzwerk bestehend aus einer Vielzahl von unterschiedlichen Akteuren im komplexen Zusammenspiel. Ständige Gesundheitsreformen aufgrund steigender Ausgaben im Gesundheitswesen sowie Fortschritte in der Medizin nehmen Einfluss auf die Informationsverarbeitung in diesem Netzwerk. Das hat zur Folge, dass immer mehr Anwendungssysteme zum Einsatz kommen, die hinsichtlich ihrer Zusammenarbeit besondere Herausforderungen stellen. Häufig können die komplexen Abläufe bei der Zusammenarbeit der Anwendungssysteme erst durch ein Modell, welches die Realität abstrahiert, verstanden werden. In diesem Zusammenhang wird das deutsche Gesundheitswesen durch ein virtuelles Gesundheitssystem modelliert, welches die Akteure des deutschen Gesundheitswesens nachbildet. Im Rahmen der vorliegenden Diplomarbeit wird die Population durch einen Generator abgebildet. Der Generator generiert anhand der Patientendaten der Population ereignisbasierte Nachrichtenprofile, die dem virtuellen Gesundheitssystem zur Weiterverarbeitung zur Verfügung gestellt werden
Exact Asymptotic Results for a Model of Sequence Alignment
Finding analytically the statistics of the longest common subsequence (LCS)
of a pair of random sequences drawn from c alphabets is a challenging problem
in computational evolutionary biology. We present exact asymptotic results for
the distribution of the LCS in a simpler, yet nontrivial, variant of the
original model called the Bernoulli matching (BM) model which reduces to the
original model in the large c limit. We show that in the BM model, for all c,
the distribution of the asymptotic length of the LCS, suitably scaled, is
identical to the Tracy-Widom distribution of the largest eigenvalue of a random
matrix whose entries are drawn from a Gaussian unitary ensemble. In particular,
in the large c limit, this provides an exact expression for the asymptotic
length distribution in the original LCS problem.Comment: 4 pages Revtex, 2 .eps figures include
Alpha-helical destabilization of the Bcl-2-BH4-domain peptide abolishes its ability to inhibit the IP3 receptor
The anti-apoptotic Bcl-2 protein is the founding member and namesake of the Bcl-2-protein family. It has recently been demonstrated that Bcl-2, apart from its anti-apoptotic role at mitochondrial membranes, can also directly interact with the inositol 1,4,5-trisphosphate receptor (IP3R), the primary Ca2+-release channel in the endoplasmic reticulum (ER). Bcl-2 can thereby reduce pro-apoptotic IP3R-mediated Ca2+ release from the ER. Moreover, the Bcl-2 homology domain 4 (Bcl-2-BH4) has been identified as essential and sufficient for this IP3R-mediated anti-apoptotic activity. In the present study, we investigated whether the reported inhibitory effect of a Bcl-2-BH4 peptide on the IP (3)R1 was related to the distinctive alpha-helical conformation of the BH4 domain peptide. We therefore designed a peptide with two glycine "hinges" replacing residues I14 and V15, of the wild-type Bcl-2-BH4 domain (Bcl-2-BH4-IV/GG). By comparing the structural and functional properties of the Bcl-2-BH4-IV/GG peptide with its native counterpart, we found that the variant contained reduced alpha-helicity, neither bound nor inhibited the IP (3)R1 channel, and in turn lost its anti-apoptotic effect. Similar results were obtained with other substitutions in Bcl-2-BH4 that destabilized the alpha-helix with concomitant loss of IP3R inhibition. These results provide new insights for the further development of Bcl-2-BH4-derived peptides as specific inhibitors of the IP3R with significant pharmacological implications
Bethe Ansatz in the Bernoulli Matching Model of Random Sequence Alignment
For the Bernoulli Matching model of sequence alignment problem we apply the
Bethe ansatz technique via an exact mapping to the 5--vertex model on a square
lattice. Considering the terrace--like representation of the sequence alignment
problem, we reproduce by the Bethe ansatz the results for the averaged length
of the Longest Common Subsequence in Bernoulli approximation. In addition, we
compute the average number of nucleation centers of the terraces.Comment: 14 pages, 5 figures (some points are clarified
First Results of Venus Express Spacecraft Observations with Wettzell
The ESA Venus Express spacecraft was observed at X-band with the Wettzell radio telescope in October-December 2009 in the framework of an assessment study of the possible contribution of the European VLBI Network to the upcoming ESA deep space missions. A major goal of these observations was to develop and test the scheduling, data capture, transfer, processing, and analysis pipeline. Recorded data were transferred from Wettzell to Metsahovi for processing, and the processed data were sent from Mets ahovi to JIVE for analysis. A turnover time of 24 hours from observations to analysis results was achieved. The high dynamic range of the detections allowed us to achieve a milliHz level of spectral resolution accuracy and to extract the phase of the spacecraft signal carrier line. Several physical parameters can be determined from these observational results with more observational data collected. Among other important results, the measured phase fluctuations of the carrier line at different time scales can be used to determine the influence of the solar wind plasma density fluctuations on the accuracy of the astrometric VLBI observations
The theory of exponential differential equations
This thesis is a model-theoretic study of exponential differential equations in the context of differential algebra. I define the theory of a set of differential equations and give an axiomatization for the theory of the exponential differential equations of split semiabelian varieties. In particular, this includes the theory of the equations satisfied by the usual complex exponential function and the Weierstrass p-functions.
The theory consists of a description of the algebraic structure on the solution sets together with necessary and sufficient conditions for a system of equations to have solutions. These conditions are stated in terms of a dimension theory; their necessity generalizes Ax’s differential field version of Schanuel’s conjecture and their sufficiency generalizes recent work of Crampin. They are shown to apply to the solving of systems of equations in holomorphic functions away from singularities, as well as in the abstract setting.
The theory can also be obtained by means of a Hrushovski-style amalgamation construction, and I give a category-theoretic account of the method.
Restricting to the usual exponential differential equation, I show that a “blurring” of Zilber’s pseudo-exponentiation satisfies the same theory. I conjecture that this theory also holds for a suitable blurring of the complex exponential maps and partially resolve the question, proving the necessity but not the sufficiency of the aforementioned conditions.
As an algebraic application, I prove a weak form of Zilber’s conjecture on intersections with subgroups (known as CIT) for semiabelian varieties. This in turn is used to show that the necessary and sufficient conditions are expressible in the appropriate first order language
Magic Angle Spinning Nuclear Magnetic Resonance Characterization of Voltage-Dependent Anion Channel Gating in Two-Dimensional Lipid Crystalline Bilayers
National Institutes of Health (U.S.) (EB001960)National Institutes of Health (EB002026
Toolbox model of evolution of metabolic pathways on networks of arbitrary topology
In prokaryotic genomes the number of transcriptional regulators is known to
quadratically scale with the total number of protein-coding genes. Toolbox
model was recently proposed to explain this scaling for metabolic enzymes and
their regulators. According to its rules the metabolic network of an organism
evolves by horizontal transfer of pathways from other species. These pathways
are part of a larger "universal" network formed by the union of all
species-specific networks. It remained to be understood, however, how the
topological properties of this universal network influence the scaling law of
functional content of genomes. In this study we answer this question by first
analyzing the scaling properties of the toolbox model on arbitrary tree-like
universal networks. We mathematically prove that the critical branching
topology, in which the average number of upstream neighbors of a node is equal
to one, is both necessary and sufficient for the quadratic scaling. Conversely,
the toolbox model on trees with exponentially expanding, supercritical topology
is characterized by the linear scaling with logarithmic corrections. We further
generalize our model to include reactions with multiple substrates/products as
well as branched or cyclic metabolic pathways. Unlike the original model the
new version employs evolutionary optimized pathways with the smallest number of
reactions necessary to achieve their metabolic tasks. Numerical simulations of
this most realistic model on the universal network from the KEGG database again
produced approximately quadratic scaling. Our results demonstrate why, in spite
of their "small-world" topology, real-life metabolic networks are characterized
by a broad distribution of pathway lengths and sizes of metabolic regulons in
regulatory networks.Comment: 34 pages, 9 figures, 2 table
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