SBML Level 3 Package: Layout ('layout')

With the development of the Systems Biology Markup Language (SBML), there now is a common standard for the exchange of dynamical models in systems biology. It has already been adopted by many applications in this field (Hucka et al., 2011, 2003; SBML Team, 2012). In 2002, we worked on an automatic layout algorithm (Wegner and Kummer, 2005). This algorithm was based on the principle that, given an SBML file, the species and reactions should be placed automatically as a network. Since there was no way to save the final layout of the network, we started developing a layout extension for SBML. In 2003, the first draft was completed and presented at the SBML workshop in St. Louis in 2004. Based on the discussions in St. Louis, Ralph Gauges finalized a first specification and implementation for libSBML (Gauges et al., 2006). During the next several SBML meetings, the layout extension was discussed in depth and also challenged by other proposals, but due to the constant support from the community (e.g., Deckard et al., 2006), it was finally accepted as a package for SBML Level 3

SBML Level 3 package: Render, Version 1, Release 1

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). This document describes the SBML Level 3 Render package that complements the SBML Level 3 Layout package and provides a means of capturing the precise rendering of the elements in a diagram. The SBML Level 3 Render package provides a flexible approach to rendering that is independent of both the underlying SBML model and the Layout information. There can be one block of render information that applies to all layouts or an additional block for each layout. Many of the elements used in the current render specification are based on corresponding elements from the SVG specification. This allows us to easily convert a combination of layout information and render information into a SVG drawing

Recommendations for collecting and analysing migration-related determinants in public health research

Background: According to the definition of the German Federal Statistical Office, about every fourth person living in Germany has a so-called migration background (MB), i.e., the person or at least one of their parents was born without German citizenship. However, MB has been defined differently in many studies. Also, the MB summarises people in different living situations, making differentiated analysis in health science more difficult. This article formulates recommendations for the collection and analysis of migration-related, as well as social and structural, determinants of health. Indicators for capturing relevant determinants of health: As part of the Improving Health Monitoring in Migrant Populations project (IMIRA), the previous approaches to operationalise and measure migration-related determinants were revised based on literature research and exchange formats, such as workshops, meetings, congress contributions, etc. Instead of MB, the country of birth of the respondents and their parents, duration of residence, citizenship(s), residence status, and German language proficiency should be recorded as minimum indicators and analysed as individual variables. Further social and structural determinants, such as socioeconomic position, working and housing conditions, or self-reported discrimination, should be included. Conclusions: In order to describe health inequalities and to specifically identify the needs of people with a history of migration, a mutual and differentiated consideration of migration-related and social determinants of health is essential

Empfehlungen zur Erhebung und Analyse migrationsbezogener Determinanten in der Public-Health-Forschung

Hintergrund: Etwa jede vierte in Deutschland lebende Person hat nach Definition des Statistischen Bundesamts einen sogenannten Migrationshintergrund (MH), d. h. die Person selbst oder mindestens ein Elternteil wurde ohne die deutsche Staatsangehörigkeit geboren. Allerdings wurde der MH in vielen Studien unterschiedlich definiert. Auch werden durch den MH Personen in unterschiedlichen Lebenslagen zusammengefasst und differenzierte gesundheitswissenschaftliche Analysen sind mit dem MH erschwert. Der Beitrag formuliert Empfehlungen zur Erhebung und Auswertung migrationsbezogener sowie sozialer und struktureller Determinanten der Gesundheit. Erfassung relevanter Gesundheitsdeterminanten: Im Rahmen des Projektes „Improving Health Monitoring in Migrant Populations (IMIRA)“ wurden die bisherigen Ansätze zur Operationalisierung und Messung migrationsbezogener Determinanten auf Grundlage von Literaturrecherchen und Austauschformaten, wie Workshops, Arbeitstreffen, Kongressbeiträgen u. ä. überarbeitet. Anstelle des MH sollten als Mindestindikatoren das Geburtsland der Befragten und deren Eltern, die Aufenthaltsdauer, die Staatsangehörigkeit(en), der Aufenthaltsstatus und Kenntnisse der deutschen Sprache erfasst und als Einzelvariablen analysiert werden. Weitere soziale und strukturelle Determinanten wie der sozioökonomische Status, Wohn- und Arbeitsbedingungen oder selbstberichtete Diskriminierung sollten einbezogen werden. Diskussion: Um gesundheitliche Ungleichheit zu beschreiben und gezielt Bedarfe von Menschen mit Migrationsgeschichte zu identifizieren, ist eine gemeinsame und differenzierte Betrachtung migrationsbezogener und sozialer Determinanten unerlässlich

Tests of model of color reconnection and a search for glueballs using gluon jets with a rapidity gap

Gluon jets with a mean energy of 22 GeV and purity of 95% are selected from hadronic Z0 decay events produced in e+e- annihilations. A subsample of these jets is identified which exhibits a large gap in the rapidity distribution of particles within the jet. After imposing the requirement of a rapidity gap, the gluon jet purity is 86%. These jets are observed to demonstrate a high degree of sensitivity to the presence of color reconnection, i.e. higher order QCD processes affecting the underlying color structure. We use our data to test three QCD models which include a simulation of color reconnection: one in the Ariadne Monte Carlo, one in the Herwig Monte Carlo, and the other by Rathsman in the Pythia Monte Carlo. We find the Rathsman and Ariadne color reconnection models can describe our gluon jet measurements only if very large values are used for the cutoff parameters which serve to terminate the parton showers, and that the description of inclusive Z0 data is significantly degraded in this case. We conclude that color reconnection as implemented by these two models is disfavored. The signal from the Herwig color reconnection model is less clear and we do not obtain a definite conclusion concerning this model. In a separate study, we follow recent theoretical suggestions and search for glueball-like objects in the leading part of the gluon jets. No clear evidence is observed for these objects.Comment: 42 pages, 18 figure

W Boson Polarisation at LEP2

Elements of the spin density matrix for W bosons in e+e- -> W+W- -> qqln events are measured from data recorded by the OPAL detector at LEP. This information is used calculate polarised differential cross-sections and to search for CP-violating effects. Results are presented for W bosons produced in e+e- collisions with centre-of-mass energies between 183 GeV and 209 GeV. The average fraction of W bosons that are longitudinally polarised is found to be (23.9 +- 2.1 +- 1.1)% compared to a Standard Model prediction of (23.9 +- 0.1)%. All results are consistent with CP conservation.Comment: 20 pages, 3 figures, Submitted to Phys. Letts.

A study of charm production in beauty decays with the OPAL detector at LEP

Using an inclusive method, BR(b -> D\bar{D}X) has been measured in hadronic Z^0 decays with the OPAL detector at LEP. The impact parameter significance of tracks opposite tagged b-jets is used to differentiate b -> D\bar{D}X decays from other decays. Using this result, the average number of charm and anti-charm quarks produced per beauty quark decay, n_c, is determined.Comment: 20 pages, 4 figure

Search for Yukawa Production of a Light Neutral Higgs Boson at LEP

Within a Two-Higgs-Doublet Model (2HDM) a search for a light Higgs boson in the mass range of 4-12 GeV has been performed in the Yukawa process e+e- -> b bbar A/h -> b bbar tau+tau-, using the data collected by the OPAL detector at LEP between 1992 and 1995 in e+e- collisions at about 91 GeV centre-of-mass energy. A likelihood selection is applied to separate background and signal. The number of observed events is in good agreement with the expected background. Within a CP-conserving 2HDM type II model the cross-section for Yukawa production depends on xiAd = |tan beta| and xihd = |sin alpha/cos beta| for the production of the CP-odd A and the CP-even h, respectively, where tan beta is the ratio of the vacuum expectation values of the Higgs doublets and alpha is the mixing angle between the neutral CP-even Higgs bosons. From our data 95% C.L. upper limits are derived for xiAd within the range of 8.5 to 13.6 and for xihd between 8.2 to 13.7, depending on the mass of the Higgs boson, assuming a branching fraction into tau+tau- of 100%. An interpretation of the limits within a 2HDM type II model with Standard Model particle content is given. These results impose constraints on several models that have been proposed to explain the recent BNL measurement of the muon anomalous magnetic moment.Comment: 24 pages, 9 figures, Submitted to Euro. Phys. J.

Measurement of triple gauge boson couplings from WW production at LEP energies up to 189 GeV

A measurement of triple gauge boson couplings is presented, based on W-pair data recorded by the OPAL detector at LEP during 1998 at a centre-of-mass energy of 189 GeV with an integrated luminosity of 183 pb^-1. After combining with our previous measurements at centre-of-mass energies of 161-183 GeV we obtain k_g=0.97 +0.20 -0.16, g_1^z=0.991 +0.060 -0.057 and lambda_g=-0.110 +0.058 -0.055, where the errors include both statistical and systematic uncertainties and each coupling is determined by setting the other two couplings to their SM values. These results are consistent with the Standard Model expectations.Comment: 28 pages, 8 figures, submitted to Eur. Phys. J.

Measurement of the Hadronic Cross-Section for the Scattering of Two Virtual Photons at LEP

The interaction of virtual photons is investigated using the reaction e+e- -> e+e- hadrons based on data taken by the OPAL experiment at e+e- centre-of-mass energies sqrt(s_ee)=189-209 GeV, for W>5 GeV and at an average Q^2 of 17.9 GeV^2. The measured cross-sections are compared to predictions of the Quark Parton Model (QPM), to the Leading Order QCD Monte Carlo model PHOJET to the NLO prediction for the reaction e+e- -> e+e-qqbar, and to BFKL calculations. PHOJET, NLO e+e- -> e+e-qqbar, and QPM describe the data reasonably well, whereas the cross-section predicted by a Leading Order BFKL calculation is too large.Comment: 30 pages, 10 figures, Submitted to Eur.Phys.J.