E-BioFlow: Different Perspectives on Scientific Workflows

We introduce a new type of workflow design system called\ud e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows

A new method of quantization of classical solutions

Using stochastic quantization method we derive equations for correlators of quantum fluctuations around the classical solution in the massless phi^4 theory. The obtained equations are then solved in the lowest orders of perturbation theory, and the first correction to the free propagator of a quantum fluctuation is calculated.Comment: 8 page

How to study basement membrane stiffness as a biophysical trigger in prostate cancer and other age-related pathologies or metabolic diseases

Here we describe a protocol that can be used to study the biophysical microenvironment related to increased thickness and stiffness of the basement membrane (BM) during age-related pathologies and metabolic disorders (e.g. cancer, diabetes, microvascular disease, retinopathy, nephropathy and neuropathy). The premise of the model is non-enzymatic crosslinking of reconstituted BM (rBM) matrix by treatment with glycolaldehyde (GLA) to promote advanced glycation endproduct (AGE) generation via the Maillard reaction. Examples of laboratory techniques that can be used to confirm AGE generation, non-enzymatic crosslinking and increased stiffness in GLA treated rBM are outlined. These include preparation of native rBM (treated with phosphate-buffered saline, PBS) and stiff rBM (treated with GLA) for determination of: its AGE content by photometric analysis and immunofluorescent microscopy, its non-enzymatic crosslinking by ((sodium dodecyl sulfate polyacrylamide gel electrophoresis)) (SDS PAGE) as well as confocal microscopy, and its increased stiffness using rheometry. The procedure described here can be used to increase the rigidity (elastic moduli, E) of rBM up to 3.2-fold, consistent with measurements made in healthy versus diseased human prostate tissue. To recreate the biophysical microenvironment associated with the aging and diseased prostate gland three prostate cell types were introduced on to native rBM and stiff rBM: RWPE-1, prostate epithelial cells (PECs) derived from a normal prostate gland; BPH-1, PECs derived from a prostate gland affected by benign prostatic hyperplasia (BPH); and PC3, metastatic cells derived from a secondary bone tumor originating from prostate cancer. Multiple parameters can be measured, including the size, shape and invasive characteristics of the 3D glandular acini formed by RWPE-1 and BPH-1 on native versus stiff rBM, and average cell length, migratory velocity and persistence of cell movement of 3D spheroids formed by PC3 cells under the same conditions. Cell signaling pathways and the subcellular localization of proteins can also be assessed

Induced two-photon decay of the 2s level and the rate of cosmological hydrogen recombination

Induced emission due to the presence of soft CMB photons slightly increases the two-photon decay rate of the 2s level of hydrogen defining the rate of cosmological recombination. This correspondingly changes the degree of ionization, the visibility function and the resulting primordial temperature anisotropies and polarization of the CMB on the percent level. These changes exceed the precision of the widely used CMBFAST and CAMB codes by more than one order of magnitude and can be easily taken into account.Comment: 5 pages, 5 figure, accepted by Astronomy and Astrophysic

Correlated many-body treatment of Breit interaction with application to cesium atomic properties and parity violation

Corrections from Breit interaction to basic properties of atomic 133Cs are determined in the framework of third-order relativistic many-body perturbation theory. The corrections to energies, hyperfine-structure constants, off-diagonal hyperfine 6S-7S amplitude, and electric-dipole matrix elements are tabulated. It is demonstrated that the Breit corrections to correlations are comparable to the Breit corrections at the Dirac-Hartree-Fock level. Modification of the parity-nonconserving (PNC) 6S-7S amplitude due to Breit interaction is also evaluated; the resulting weak charge of $^{133}$Cs shows no significant deviation from the prediction of the standard model of elementary particles. The neutron skin correction to the PNC amplitude is also estimated to be -0.2% with an error bound of 30% based on the analysis of recent experiments with antiprotonic atoms. The present work supplements publication [A. Derevianko, Phys. Rev. Lett. 85, 1618 (2000)] with a discussion of the formalism and provides additional numerical results and updated discussion of parity violation.Comment: 16 pages; 5 figs; submitted to Phys. Rev.

One- and two-proton transfer reactions with vibrational Nuclei

We extend a semiclassical model of transfer reactions to the case in which one of the collision partners is a vibrational nucleus. The model is applied to one- and two-proton stripping reactions in the 37Cl + 98Mo system, for which a rapid transition from normal to anomalous slope in the two proton transfer reaction at energies around the Coulomb barrier is experimentally observed. This behavior is satisfactorily reproduced by the present extension of the model.Comment: LaTeX, 10 pages, 1 figure (PostScript

Role of Present and Future Atomic Parity Violation Experiments in Precision Electroweak Tests

Recent reanalyses of the atomic physics effects on the weak charge in cesium have led to a value in much closer agreement with predictions of the Standard Model. We review precision electroweak tests, their implications for upper bounds on the mass of the Higgs boson, possible ways in which these bounds may be circumvented, and the requirements placed upon accuracy of future atomic parity violation experiments by these considerations.Comment: 10 pages, LaTeX, 1 figure, to be submitted to Physical Review D, new data on neutrino deep inelastic scattering include

Evaluation of the self-energy correction to the g-factor of S states in H-like ions

A detailed description of the numerical procedure is presented for the evaluation of the one-loop self-energy correction to the $g$-factor of an electron in the $1s$ and $2s$ states in H-like ions to all orders in $Z\alpha$.Comment: Final version, December 30, 200

SigWinR; the SigWin-detector updated and ported to R

<p>Abstract</p> <p>Background</p> <p>Our SigWin-detector discovers significantly enriched windows of (genomic) elements in any sequence of values (genes or other genomic elements in a DNA sequence) in a fast and reproducible way. However, since it is grid based, only (life) scientists with access to the grid can use this tool. Therefore and on request, we have developed the SigWinR package which makes the SigWin-detector available to a much wider audience. At the same time, we have introduced several improvements to its algorithm as well as its functionality, based on the feedback of SigWin-detector end users.</p> <p>Findings</p> <p>To allow usage of the SigWin-detector on a desktop computer, we have rewritten it as a package for R: SigWinR. R is a free and widely used multi platform software environment for statistical computing and graphics. The package can be installed and used on all platforms for which R is available. The improvements involve: a visualization of the input-sequence values supporting the interpretation of Ridgeograms; a visualization allowing for an easy interpretation of enriched or depleted regions in the sequence using windows of pre-defined size; an option that allows the analysis of circular sequences, which results in rectangular Ridgeograms; an application to identify regions of co-altered gene expression (ROCAGEs) with a real-life biological use-case; adaptation of the algorithm to allow analysis of non-regularly sampled data using a constant window size in physical space without resampling the data. To achieve this, support for analysis of windows with an even number of elements was added.</p> <p>Conclusion</p> <p>By porting the SigWin-detector as an R package, SigWinR, improving its algorithm and functionality combined with adequate performance, we have made SigWin-detector more useful as well as more easily accessible to scientists without a grid infrastructure.</p

Baryon magnetic moments in the effective quark Lagrangian approach

An effective quark Lagrangian is derived from first principles through bilocal gluon field correlators. It is used to write down equations for baryons, containing both perturbative and nonperturbative fields. As a result one obtains magnetic moments of octet and decuplet baryons without introduction of constituent quark masses and using only string tension as an input. Magnetic moments come out on average in reasonable agreement with experiment, except for nucleons and $\Sigma^-$. The predictions for the proton and neutron are shown to be in close agreement with the empirical values once we choose the string tension such to yield the proper nucleon mass. Pionic corrections to the nucleon magnetic moments have been estimated. In particular, the total result of the two-body current contributions are found to be small. Inclusion of the anomalous magnetic moment contributions from pion and kaon loops leads to an improvement of the predictions.Comment: 24 pages Revte