Noncommutative Geometries and Gravity

We briefly review ideas about ``noncommutativity of space-time'' and approaches toward a corresponding theory of gravity.Comment: 18 pages, to appear in the Proceedings of the Third Mexican Meeting on Mathematical and Experimental Physics, Symposium on Gravitation and Cosmology, Mexico City, 10-14 September 200

Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation

Background: Manual curation of experimental data from the biomedical literature is an expensive and time-consuming endeavor. Nevertheless, most biological knowledge bases still rely heavily on manual curation for data extraction and entry. Text mining software that can semi- or fully automate information retrieval from the literature would thus provide a significant boost to manual curation efforts. Results: We employ the Textpresso category-based information retrieval and extraction system http://www.textpresso.org webcite, developed by WormBase to explore how Textpresso might improve the efficiency with which we manually curate C. elegans proteins to the Gene Ontology's Cellular Component Ontology. Using a training set of sentences that describe results of localization experiments in the published literature, we generated three new curation task-specific categories (Cellular Components, Assay Terms, and Verbs) containing words and phrases associated with reports of experimentally determined subcellular localization. We compared the results of manual curation to that of Textpresso queries that searched the full text of articles for sentences containing terms from each of the three new categories plus the name of a previously uncurated C. elegans protein, and found that Textpresso searches identified curatable papers with recall and precision rates of 79.1% and 61.8%, respectively (F-score of 69.5%), when compared to manual curation. Within those documents, Textpresso identified relevant sentences with recall and precision rates of 30.3% and 80.1% (F-score of 44.0%). From returned sentences, curators were able to make 66.2% of all possible experimentally supported GO Cellular Component annotations with 97.3% precision (F-score of 78.8%). Measuring the relative efficiencies of Textpresso-based versus manual curation we find that Textpresso has the potential to increase curation efficiency by at least 8-fold, and perhaps as much as 15-fold, given differences in individual curatorial speed. Conclusion: Textpresso is an effective tool for improving the efficiency of manual, experimentally based curation. Incorporating a Textpresso-based Cellular Component curation pipeline at WormBase has allowed us to transition from strictly manual curation of this data type to a more efficient pipeline of computer-assisted validation. Continued development of curation task-specific Textpresso categories will provide an invaluable resource for genomics databases that rely heavily on manual curation

Kinetics and the Theoretical Aspects of Drug Release from PLA/HAp Thin Films

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.The theory of dissolution kinetics of gentamicin from polylactic acid-hydroxyapatite thin film composites is spotlighted with the combination of diffusion and polymer degradation modeling. The use of various mathematical models, characterizing diffusion, dissolution or/and erosion prevalence as well as a mix of dissolution-diffusion rate processes were employed in order to compare theory with experimental data. A number of factors influence the release kinetics of gentamicin from medical drug release systems and devices. It is difficult to have a single mathematical model that takes all these factors into account. It is shown that the degradation of the polymer matrix plays the biggest role in the release kinetics of polymer-ceramics thin film composites. It was also observed that multistage drug release form these devices depends also on the degradation kinetics of the polymer matrix. The effect of pH and device sizes were not studied but could also be of interest in future studies

Supernova explosions and the birth of neutron stars

We report here on recent progress in understanding the birth conditions of neutron stars and the way how supernovae explode. More sophisticated numerical models have led to the discovery of new phenomena in the supernova core, for example a generic hydrodynamic instability of the stagnant supernova shock against low-mode nonradial deformation and the excitation of gravity-wave activity in the surface and core of the nascent neutron star. Both can have supportive or decisive influence on the inauguration of the explosion, the former by improving the conditions for energy deposition by neutrino heating in the postshock gas, the latter by supplying the developing blast with a flux of acoustic power that adds to the energy transfer by neutrinos. While recent two-dimensional models suggest that the neutrino-driven mechanism may be viable for stars from about 8 solar masses to at least 15 solar masses, acoustic energy input has been advocated as an alternative if neutrino heating fails. Magnetohydrodynamic effects constitute another way to trigger explosions in connection with the collapse of sufficiently rapidly rotating stellar cores, perhaps linked to the birth of magnetars. The global explosion asymmetries seen in the recent simulations offer an explanation of even the highest measured kick velocities of young neutron stars.Comment: 10 pages, 8 figures, 19 ps files; to be published in Proc. of Conf. "40 Years of Pulsars: Millisecond Pulsars, Magnetars, and More", August 12-17, 2007, McGill Univ., Montreal, Canada; high-resolution images can be obtained upon request; incorrect panel in fig.8 replace

Relativistic magnetotransport in graphene

We study the thermal and electric transport of a fluid of interacting Dirac fermions as they arise in single-layer graphene. We include Coulomb interactions, a dilute density of charged impurities and the presence of a magnetic field to describe both the static and the low frequency response as a function of temperature T and chemical potential mu. In the critical regime mu << T where both bands above and below the Dirac point contribute to transport we find pronounced deviations from Fermi liquid behavior, universal, collision-dominated values for transport coefficients and a cyclotron resonance of collective nature. In the collision-dominated high temperature regime the linear thermoelectric transport coefficients are shown to obey the constraints of relativistic magnetohydrodynamics which we derive microscopically from Boltzmann theory. The latter also allows us to describe the crossover to disorder-dominated Fermi liquid behavior at large doping and low temperatures, as well as the crossover to the ballistic regime at high fields.Comment: Proceedings of the Landau Memorial Conference 200

Introduction to the Bethe ansatz II

Building on the fundamentals introduced in part I, we employ the Bethe ansatz to study some ground-state properties (energy, magnetization, susceptibility) of the one-dimensional s=1/2 Heisenberg antiferromagnet in zero and nonzero magnetic field. The 2-spinon triplet and singlet excitations from the zero-field ground state are discussed in detail, and their energies are calculated for finite and infinite chains. Procedures for the numerical calculation of real and complex solutions of the Bethe ansatz equations are discussed and applied. The paper is designed as a tutorial for beginning graduate students. It includes 10 problems for further study.Comment: 9 pages, 5 figure

enabling a research data management beyond data heterogeneity

A primary goal of a research infrastructure for data management should be to enable efficient data discovery and integration of heterogeneous data. The German Federation for Biological Data (GFBio) was envisioned by this goal. The basic component, that enables such interoperability and serves as a backbone for such a platform, is the GFBio Terminology Service (GFBio TS). It acts as a semantic platform for accessing, developing and reasoning over terminological resources within the biological and environmental domain. A RESTful API gives access to these terminological resources in a uniform way regardless of their degree of complexity and whether they are internally stored or externally accessed through their web services. Additionally, a set of widgets with an intrinsic API connection are made available for an easy integration in applications and web interfaces. Based on the requirements of the GFBio partners, we describe the added value that is provided by the GFBio Terminology Service with practical scenarios but also, what challenges we still face. We conclude by describing our current activities and future developments

Two-photon laser scanning fluorescence microscopy using photonic crystal fibre

We report the application of a simple yet powerful modular pulse compression system, based on photonic crystal fibres which improves upon incumbent twophoton laser scanning fluorescence microscopy techniques. This system provided more than a 7-fold increase in fluorescence yield when compared with a commercial two-photon microscopy system. From this, we infer pulses of infrared radiaton of less than 35 fs duration reaching the sample

Isospectrality of spherical MHD dynamo operators: pseudo-Hermiticity and a no-go theorem

The isospectrality problem is studied for the operator of the spherical hydromagnetic alpha^2-dynamo. It is shown that this operator is formally pseudo-Hermitian (J-symmetric) and lives in a Krein space. Based on the J-symmetry, an operator intertwining Ansatz with first-order differential intertwining operators is tested for its compatibility with the structure of the alpha^2-dynamo operator matrix. An intrinsic structural inconsistency is obtained in the set of associated matrix Riccati equations. This inconsistency is interpreted as a no-go theorem which forbids the construction of isospectral alpha^2-dynamo operator classes with the help of first-order differential intertwining operators.Comment: 13 pages, LaTeX2e, improved references, to appear in J. Math. Phy

Dynamics of quantum spin systems in dimer and valence-bond solid ground states stabilized by competing interactions

For special coupling ratios, the one-dimensional (1D) s=1/2 Heisenberg model with antiferromagnetic nearest and next-nearest neighbor interactions has a pure dimer ground state, and the 1D s=1 Heisenberg model with antiferromagnetic bilinear and biquadratic interactions has an exact valence-bond-solid ground state. The recursion method is used to calculate the T=0 spin dynamic structure factor for both models and, for the s=1/2 model, also the dimer dynamic structure factor. New results for line shapes and dynamically relevant dispersions are obtained.Comment: RevTex file, 3 ps figure