PayDIBI: Pay-as-you-go data integration for bioinformatics

Background: Scientific research in bio-informatics is often data-driven and supported by biolog- ical databases. In a growing number of research projects, researchers like to ask questions that require the combination of information from more than one database. Most bio-informatics papers do not detail the integration of different databases. As roughly 30% of all tasks in workflows are data transformation tasks, database integration is an important issue. Integrating multiple data sources can be difficult. As data sources are created, many design decisions are made by their creators. Methods: Our research is guided by two use cases: homologues, the representation and integration of groupings; metabolomics integration, with a focus on the TCA cycle. Results: We propose to approach the time consuming problem of integrating multiple biological databases through the principles of ‘pay-as-you-go’ and ‘good-is-good-enough’. By assisting the user in defining a knowledge base of data mapping rules, trust information and other evidence we allow the user to focus on the work, and put in as little effort as is necessary for the integration. Through user feedback on query results and trust assessments, the integration can be improved upon over time. Conclusions: We conclude that this direction of research is worthy of further exploration

Optical Continuum and Emission-Line Variability of Seyfert 1 Galaxies

We present the light curves obtained during an eight-year program of optical spectroscopic monitoring of nine Seyfert 1 galaxies: 3C 120, Akn 120, Mrk 79, Mrk 110, Mrk 335, Mrk 509, Mrk 590, Mrk 704, and Mrk 817. All objects show significant variability in both the continuum and emission-line fluxes. We use cross-correlation analysis to derive the sizes of the broad Hbeta-emitting regions based on emission-line time delays, or lags. We successfully measure time delays for eight of the nine sources, and find values ranging from about two weeks to a little over two months. Combining the measured lags and widths of the variable parts of the emission lines allows us to make virial mass estimates for the active nucleus in each galaxy. The virial masses are in the range 10^{7-8} solar masses.Comment: 24 pages, 16 figures. Accepted for publication in Ap

Chiral two-loop pion-pion scattering parameters from crossing-symmetric constraints

Constraints on the parameters in the one- and two-loop pion-pion scattering amplitudes of standard chiral perturbation theory are obtained from explicitly crossing-symmetric sum rules. These constraints are based on a matching of the chiral amplitudes and the physical amplitudes at the symmetry point of the Mandelstam plane. The integrals over absorptive parts appearing in the sum rules are decomposed into crossing-symmetric low- and high-energy components and the chiral parameters are finally related to high-energy absorptive parts. A first application uses a simple model of these absorptive parts. The sensitivity of the results to the choice of the energy separating high and low energies is examined with care. Weak dependence on this energy is obtained as long as it stays below ~560 MeV. Reliable predictions are obtained for three two-loop parameters.Comment: 23 pages, 4 figures in .eps files, Latex (RevTex), our version of RevTex runs under Latex2.09, submitted to Phys. Rev. D,minor typographical corrections including the number at the end of the abstract, two sentences added at the end of Section 5 in answer to a referee's remar

A discrete time relativistic Toda lattice

Four integrable symplectic maps approximating two Hamiltonian flows from the relativistic Toda hierarchy are introduced. They are demostrated to belong to the same hierarchy and to examplify the general scheme for symplectic maps on groups equiped with quadratic Poisson brackets. The initial value problem for the difference equations is solved in terms of a factorization problem in a group. Interpolating Hamiltonian flows are found for all the maps.Comment: 32 pages, LaTe

Incremental data uncertainty handling using evidence combination: a case study on maritime data reasoning

Semantic incompatibility is a conflict that occurs in the meanings of data. In this paper, we propose an approach for data cleaning by resolving semantic incompatibility. Our approach applies a dynamic and incremental enhancement of data quality. It checks the coherency/conflict of the newly recorded facts/relations against the existing ones. It reasons over the existing information and comes up with new discovered facts/relations. We choose maritime data cleaning as a validation scenario

Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency

A new case of 3-hydroxyacyl-CoA dehydrogenase deficiency is described with a relatively benign course

Testing the ΔS=ΔQ\Delta S=\Delta Q Rule with Exclusive Semi-Leptonic Kaon Decays

We consider the possibility of violations of the selection rule $\Delta S=\Delta Q$ at an appreciable level in {\it exclusive} semi-leptonic decays of Kaons. At $\Phi$-Factories, intense Kaon beams will be available and will probe among others, the semi-leptonic decays $K_{l4}$ and $K_{l3\gamma}$ in addition to $K_{l3}$ and could provide novel testing grounds for the $\Delta S=\Delta Q$ rule. In particular, the branching ratio of $K_{l3\gamma}$ is non-negligible and could be used to probe new phenomena associated with the violation of this selection rule. Furthermore, we modify certain di-lepton event rate ratios and asymmetries and time asymmetries that have been constructed by Dass and Sarma for di-lepton events from Beon decays to test the $\Delta B=\Delta Q$ at the $\Upsilon (4S)$, to the Kaon system at the $\phi(1020)$. We find that the large width of the $K_S$ relative to that of $K_L$ plays an important role in enhancing some of the time asymmetries.Comment: 10 pages, Plain Latex, To be run twice

The Low Energy Expansion for Pion-Pion Scattering and Crossing Symmetry in Dispersion Relations

We show that a suitable setting for comparison of the low-energy representation for pion-pion scattering amplitudes, with dispersive representation for these amplitudes, is provided by certain manifestly crossing symmetric dispersion relations. We begin with a discussion of fixed-t dispersion relations and discuss the origin of crossing constraints that arise in this context when we consider resonance saturation with certain $l\geq 2$ states. We demonstrate that the approach advocated here does not require us to enforce such constraints. Our results are contrasted with those from fixed-t dispersion relations. We finally discuss the numerical import of our results.Comment: 24 pages plain LaTeX, to be run twic

Central Masses and Broad-Line Region Sizes of Active Galactic Nuclei. II. A Homogeneous Analysis of a Large Reverberation-Mapping Database

We present improved black hole masses for 35 active galactic nuclei (AGNs) based on a complete and consistent reanalysis of broad emission-line reverberation-mapping data. From objects with multiple line measurements, we find that the highest precision measure of the virial product is obtained by using the cross-correlation function centroid (as opposed to the cross-correlation function peak) for the time delay and the line dispersion (as opposed to full width half maximum) for the line width and by measuring the line width in the variable part of the spectrum. Accurate line-width measurement depends critically on avoiding contaminating features, in particular the narrow components of the emission lines. We find that the precision (or random component of the error) of reverberation-based black hole mass measurements is typically around 30%, comparable to the precision attained in measurement of black hole masses in quiescent galaxies by gas or stellar dynamical methods. Based on results presented in a companion paper by Onken et al., we provide a zero-point calibration for the reverberation-based black hole mass scale by using the relationship between black hole mass and host-galaxy bulge velocity dispersion. The scatter around this relationship implies that the typical systematic uncertainties in reverberation-based black hole masses are smaller than a factor of three. We present a preliminary version of a mass-luminosity relationship that is much better defined than any previous attempt. Scatter about the mass-luminosity relationship for these AGNs appears to be real and could be correlated with either Eddington ratio or object inclination.Comment: 61 pages, including 8 Tables and 16 Figures. Accepted for publication in The Astrophysical Journa

Effect of Animal and Industrial Trans Fatty Acids on HDL and LDL Cholesterol Levels in Humans – A Quantitative Review

Background: Trans fatty acids are produced either by industrial hydrogenation or by biohydrogenation in the rumens of cows and sheep. Industrial trans fatty acids lower HDL cholesterol, raise LDL cholesterol, and increase the risk of coronary heart disease. The effects of conjugated linoleic acid and trans fatty acids from ruminant animals are less clear. We reviewed the literature, estimated the effects trans fatty acids from ruminant sources and of conjugated trans linoleic acid (CLA) on blood lipoproteins, and compared these with industrial trans fatty acids. Methodology/Principal Findings: We searched Medline and scanned reference lists for intervention trials that reported effects of industrial trans fatty acids, ruminant trans fatty acids or conjugated linoleic acid on LDL and HDL cholesterol in humans. The 39 studies that met our criteria provided results of 29 treatments with industrial trans fatty acids, 6 with ruminant trans fatty acids and 17 with CLA. Control treatments differed between studies; to enable comparison between studies we recalculated for each study what the effect of trans fatty acids on lipoprotein would be if they isocalorically replaced cis mono unsaturated fatty acids. In linear regression analysis the plasma LDL to HDL cholesterol ratio increased by 0.055 (95% CI 0.044-0.066) for each % of dietary energy from industrial trans fatty acids replacing cis monounsaturated fatty acids The increase in the LDL to HDL ratio for each % of energy was 0.038 (95% CI 0.012-0.065) for ruminant trans fatty acids, and 0.043 (95% CI 0.012-0.074) for conjugated linoleic acid (p = 0.99 for difference between CLA and industrial trans fatty acids; p = 0.37 for ruminant versus industrial trans fatty acids). Conclusions/Significance: Published data suggest that all fatty acids with a double bond in the trans configuration raise the ratio of plasma LDL to HDL cholesterol