On integration of the Kowalevski gyrostat and the Clebsch problems

For the Kowalevski gyrostat change of variables similar to that of the Kowalevski top is done. We establish one to one correspondence between the Kowalevski gyrostat and the Clebsch system and demonstrate that Kowalevski variables for the gyrostat practically coincide with elliptic coordinates on sphere for the Clebsch case. Equivalence of considered integrable systems allows to construct two Lax matrices for the gyrostat using known rational and elliptic Lax matrices for the Clebsch model. Associated with these matrices solutions of the Clebsch system and, therefore, of the Kowalevski gyrostat problem are discussed. The Kotter solution of the Clebsch system in modern notation is presented in detail.Comment: LaTeX, 24 page

(Missing) Concept Discovery in Heterogeneous Information Networks

This article proposes a new approach to extract existing (or detect missing) concepts from a loosely integrated collection of information units by means of concept graph detection. Thereby a concept graph defines a concept by a quasi bipartite sub-graph of a bigger network with the members of the concept as the first vertex partition and their shared aspects as the second vertex partition. Once the concepts have been extracted they can be used to create higher level representations of the data. Concept graphs further allow the discovery of missing concepts, which could lead to new insights by connecting seemingly unrelated information units

Yeast chassis design for production of dicarboxylic acids

Saccharomyces cerevisiae is a widely used microorganism for industrial biotechnology that has great potential to replace traditional petrochemical synthesis. Optimization of cell factories for production of different biotechnological products is still a cost and time inefficient process. Availability of pre-optimized yeast chassis cells, with improved precursor supply, will overcome such hurdles. Building upon this premise, we have developed a framework for rational design of chassis strains combining genome-scale metabolic models with a multi-objective metaheuristic approach. Here, we present the non-intuitive gene deletion targets optimized for growth-product coupled production of a family of C4-dicarboxylic acids, namely fumaric, succinic and malic acids. Several multi-gene deletion strains, including the chassis cell and the final producer strains, were implemented and experimentally tested. The strains encompassing the chassis backbone produce higher yields of respective targeted compounds than those containing merely the intuitive gene deletion(s). Taking advantage of the growth-product coupled design, best producing strains have been improved by adaptive laboratory evolution. As a proof-of-concept, we have generated pre-optimized chassis yeast cells for enhanced production of C4-dicarboxylic acids, hence showing that modular design strategies may contribute to accelerate cell factory development.info:eu-repo/semantics/publishedVersio

An Algebraic Approach for Decoding Spread Codes

In this paper we study spread codes: a family of constant-dimension codes for random linear network coding. In other words, the codewords are full-rank matrices of size (k x n) with entries in a finite field F_q. Spread codes are a family of optimal codes with maximal minimum distance. We give a minimum-distance decoding algorithm which requires O((n-k)k^3) operations over an extension field F_{q^k}. Our algorithm is more efficient than the previous ones in the literature, when the dimension k of the codewords is small with respect to n. The decoding algorithm takes advantage of the algebraic structure of the code, and it uses original results on minors of a matrix and on the factorization of polynomials over finite fields

Asymptotic bounds for the sizes of constant dimension codes and an improved lower bound

We study asymptotic lower and upper bounds for the sizes of constant dimension codes with respect to the subspace or injection distance, which is used in random linear network coding. In this context we review known upper bounds and show relations between them. A slightly improved version of the so-called linkage construction is presented which is e.g. used to construct constant dimension codes with subspace distance $d=4$, dimension $k=3$ of the codewords for all field sizes $q$, and sufficiently large dimensions $v$ of the ambient space, that exceed the MRD bound, for codes containing a lifted MRD code, by Etzion and Silberstein.Comment: 30 pages, 3 table

Conformational dynamics of the tetracycline-binding aptamer

The conformational dynamics induced by ligand binding to the tetracycline-binding aptamer is monitored via stopped-flow fluorescence spectroscopy and time-correlated single photon counting experiments. The fluorescence of the ligand is sensitive to changes within the tertiary structure of the aptamer during and after the binding process. In addition to the wild-type aptamer, the mutants A9G, A13U and A50U are examined, where bases important for regulation are changed to inhibit the aptamer’s function. Our results suggest a very fast two-step-mechanism for the binding of the ligand to the aptamer that can be interpreted as a binding step followed by a reorganization of the aptamer to accommodate the ligand. Binding to the two direct contact points A13 and A50 was found to occur in the first binding step. The exchange of the structurally important base A9 for guanine induces an enormous deceleration of the overall binding process, which is mainly rooted in an enhancement of the back reaction of the first binding step by several orders of magnitude. This indicates a significant loss of tertiary structure of the aptamer in the absence of the base A9, and underlines the importance of pre-organization on the overall binding process of the tetracycline-binding aptamer

A fast and efficient translational control system for conditional expression of yeast genes

A new artificial regulatory system for essential genes in yeast is described. It prevents translation of target mRNAs upon tetracycline (tc) binding to aptamers introduced into their 5'UTRs. Exploiting direct RNA–ligand interaction renders auxiliary protein factors unnecessary. Therefore, our approach is strain independent and not susceptible to interferences by heterologous expressed regulatory proteins. We use a simple PCR-based strategy, which allows easy tagging of any target gene and the level of gene expression can be adjusted due to various tc aptamer-regulated promoters. As proof of concept, five differently expressed genes were targeted, two of which could not be regulated previously. In all cases, adding tc completely prevented growth and, as shown for Nop14p, rapidly abolished de novo protein synthesis providing a powerful tool for conditional regulation of yeast gene expression

Status of the GEO600 gravitational wave detector

The GEO600 laser interferometric gravitational wave detector is approaching the end of its commissioning phase which started in 1995.During a test run in January 2002 the detector was operated for 15 days in a power-recycled michelson configuration. The detector and environmental data which were acquired during this test run were used to test the data analysis code. This paper describes the subsystems of GEO600, the status of the detector by August 2002 and the plans towards the first science run

Upper limits on the strength of periodic gravitational waves from PSR J1939+2134

The first science run of the LIGO and GEO gravitational wave detectors presented the opportunity to test methods of searching for gravitational waves from known pulsars. Here we present new direct upper limits on the strength of waves from the pulsar PSR J1939+2134 using two independent analysis methods, one in the frequency domain using frequentist statistics and one in the time domain using Bayesian inference. Both methods show that the strain amplitude at Earth from this pulsar is less than a few times $10^{-22}$.Comment: 7 pages, 1 figure, to appear in the Proceedings of the 5th Edoardo Amaldi Conference on Gravitational Waves, Tirrenia, Pisa, Italy, 6-11 July 200