The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’)

Spherically Symmetric Simulation with Boltzmann Neutrino Transport of Core Collapse and Post-Bounce Evolution of a 15 Solar Mass Star

We present a spherically symmetric, Newtonian core-collapse simulation of a 15 solar mass star with a 1.28 solar mass iron core. The time-, energy-, and angle-dependent transport of electron neutrinos and antineutrinos was treated with a new code which iteratively solves the Boltzmann equation and the equations for neutrino number, energy and momentum to order O(v/c) in the velocity v of the stellar medium. The supernova shock expands to a maximum radius of 350 km instead of only about 240 km as in a comparable calculation with multi-group flux-limited diffusion (MGFLD) by Bruenn, Mezzacappa, & Dineva (1995). This may be explained by stronger neutrino heating due to the more accurate transport in our model. Nevertheless, after 180 ms of expansion the shock finally recedes to a radius around 250 km (compared to about 170 km in the MGFLD run). The effect of an accurate neutrino transport is helpful, but not large enough to cause an explosion of the considered 15 solar mass star. Therefore postshock convection and/or an enhancement of the core neutrino luminosity by convection or reduced neutrino opacities in the neutron star seem necessary for neutrino-driven explosions of such stars. We find an electron fraction Y_e > 0.5 in the neutrino-heated matter, which suggests that the overproduction problem of neutron-rich nuclei with mass numbers around A = 90 in exploding models may be absent when a Boltzmann solver is used for the electron neutrino and antineutrino transport.Comment: 6 pages, LaTex, 3 encapsulated postscript figures, revised and shortened version. Astrophys. J., Letters, accepte

General-Relativistic MHD for the Numerical Construction of Dynamical Spacetimes

We assemble the equations of general relativistic magnetohydrodynamics (MHD) in 3+1 form. These consist of the complete coupled set of Maxwell equations for the electromagnetic field, Einstein's equations for the gravitational field, and the equations of relativistic MHD for a perfectly conducting ideal gas. The adopted form of the equations is suitable for evolving numerically a relativistic MHD fluid in a dynamical spacetime characterized by a strong gravitational field.Comment: 8 pages; scheduled for March 10 issue of Ap

Electron Neutrino Pair Annihilation: A New Source for Muon and Tau Neutrinos in Supernovae

We show that in a supernova core the annihilation process nu_e nu_e-bar -> nu_{mu,tau} nu_{mu,tau}-bar is always more important than the traditional reaction e^+ e^- -> nu_{mu,tau} nu_{mu,tau}-bar as a source for muon and tau neutrino pairs. We study the impact of the new process by means of a Monte Carlo transport code with a static stellar background model and by means of a self-consistent hydrodynamical simulation with Boltzmann neutrino transport. Nucleon bremsstrahlung NN -> NN nu_{mu,tau} nu_{mu,tau}-bar is also included as another important source term. Taking into account nu_e nu_e-bar -> nu_{mu,tau} nu_{mu,tau}-bar increases the nu_mu and nu_tau luminosities by as much as 20% while the spectra remain almost unaffected. In our hydrodynamical simulation the shock was somewhat weakened. Elastic nu_{mu,tau} nu_e and nu_{mu,tau} nu_e scattering is not negligible but less important than nu_{mu,tau} e^+ or e^- scattering. Its influence on the nu_{mu,tau} fluxes and spectra is small after all other processes have been included.Comment: 11 pages, 9 eps-figs, submitted to Ap

Towards Gravitational Wave Signals from Realistic Core Collapse Supernova Models

We have computed the gravitational wave signal from supernova core collapse using the presently most realistic input physics available. We start from state-of-the-art progenitor models of rotating and non-rotating massive stars, and simulate the dynamics of their core collapse by integrating the equations of axisymmetric hydrodynamics together with the Boltzmann equation for the neutrino transport including an elaborate description of neutrino interactions, and a realistic equation of state. We compute the quadrupole wave amplitudes, the Fourier wave spectra, the amount of energy radiated in form of gravitational waves, and the S/N ratios for the LIGO and the tuned Advanced LIGO interferometers resulting both from non-radial mass motion and anisotropic neutrino emission. The simulations demonstrate that the dominant contribution to the gravitational wave signal is produced by neutrino-driven convection behind the supernova shock. For stellar cores rotating at the extreme of current stellar evolution predictions, the core-bounce signal is detectable with advanced LIGO up to a distance of 5kpc, whereas the signal from post-shock convection is observable up to a distance of about 100kpc. If the core is non-rotating its gravitational wave emission can be measured up to a distance of 15kpc, while the signal from the Ledoux convection in the deleptonizing, nascent neutron star can be detected up to a distance of 10kpc. Both kinds of signals are generically produced by convection in any core collapse supernova.Comment: 9 pages, 13 figures, Latex, submitted to ApJ, error in ps-file fixed; figures in full resolution are available upon reques

Genome information management and integrated data analysis with HaloLex

HaloLex is a software system for the central management, integration, curation, and web-based visualization of genomic and other -omics data for any given microorganism. The system has been employed for the manual curation of three haloarchaeal genomes, namely Halobacterium salinarum (strain R1), Natronomonas pharaonis, and Haloquadratum walsbyi. HaloLex, in particular, enables the integrated analysis of genome-wide proteomic results with the underlying genomic data. This has proven indispensable to generate reliable gene predictions for GC-rich genomes, which, due to their characteristically low abundance of stop codons, are known to be hard targets for standard gene finders, especially concerning start codon assignment. The proteomic identification of more than 600 N-terminal peptides has greatly increased the reliability of the start codon assignment for Halobacterium salinarum. Application of homology-based methods to the published genome of Haloarcula marismortui allowed to detect 47 previously unidentified genes (a problem that is particularly serious for short protein sequences) and to correct more than 300 start codon misassignments

The bar-mode instability in differentially rotating neutron stars: Simulations in full general relativity

We study the dynamical stability against bar-mode deformation of rapidly spinning neutron stars with differential rotation. We perform fully relativistic 3D simulations of compact stars with $M/R \geq 0.1$, where $M$ is the total gravitational mass and $R$ the equatorial circumferential radius. We adopt an adiabatic equation of state with adiabatic index $\Gamma=2$. As in Newtonian theory, we find that stars above a critical value of $\beta \equiv T/W$ (where $T$ is the rotational kinetic energy and $W$ the gravitational binding energy) are dynamically unstable to bar formation. For our adopted choices of stellar compaction and rotation profile, the critical value of $\beta = \beta_{dGR}$ is $\sim 0.24-0.25$, only slightly smaller than the well-known Newtonian value $\sim 0.27$ for incompressible Maclaurin spheroids. The critical value depends only very weakly on the degree of differential rotation for the moderate range we surveyed. All unstable stars form bars on a dynamical timescale. Models with sufficiently large $\beta$ subsequently form spiral arms and eject mass, driving the remnant to a dynamically stable state. Models with moderately large $\beta \gtrsim \beta_{dGR}$ do not develop spiral arms or eject mass but adjust to form dynamically stable ellipsoidal-like configurations. If the bar-mode instability is triggered in supernovae collapse or binary neutron star mergers, it could be a strong and observable source of gravitational waves. We determine characteristic wave amplitudes and frequencies.Comment: 17 pages, accepted for publication in AP

Isolated and Combined Effects of Electroacupuncture and Meditation in Reducing Experimentally Induced Ischemic Pain: A Pilot Study

Acupuncture and meditation are promising treatment options for clinical pain. However, studies investigating the effects of these methods on experimental pain conditions are equivocal. Here, the effects of electroacupuncture (EA) and meditation on the submaximum effort tourniquet technique (SETT), a well-established, opiate-sensitive pain paradigm in experimental placebo research were studied. Ten experienced meditators (6 male subjects) and 13 nonmeditators (6 male subjects) were subjected to SETT (250 mmHG) on one baseline (SETT only) and two treatment days (additional EA contralaterally to the SETT, either at the leg on ST36 and LV3 or at the arm on LI4 and LI10 in randomized order). Numeric Rating Scale (NRS) ratings (scale 0–10) were recorded every 3 min. During baseline, meditation induced significantly greater pain tolerance in meditators when compared with the control group. Both the EA conditions significantly increased pain tolerance and reduced pain ratings in controls. Furthermore, EA diminished the group difference in pain sensitivity, indicating that meditators had no additional benefit from acupuncture. The data suggest that EA as a presumable bottom-up process may be as effective as meditation in controlling experimental SETT pain. However, no combined effect of both the techniques could be observed

The influence of a series of five dry cupping treatments on pain and mechanical thresholds in patients with chronic non-specific neck pain : a randomised controlled pilot study

In this preliminary trial we investigated the effects of dry cupping, an ancient method for treating pain syndromes, on patients with chronic non-specific neck pain. Sensory mechanical thresholds and the participants’ self-reported outcome measures of pain and quality of life were evaluated. Fifty patients (50.5 ± 11.9 years) were randomised to a treatment group (TG) or a waiting-list control group (WL). Patients in the TG received a series of 5 cupping treatments over a period of 2 weeks; the control group did not. Self-reported outcome measures before and after the cupping series included the following: Pain at rest (PR) and maximal pain related to movement (PM) on a 100-mm visual analogue scale (VAS), pain diary (PD) data on a 0-10 numeric rating scale (NRS), Neck Disability Index (NDI), and health-related quality of life (SF-36). In addition, the mechanical-detection thresholds (MDT), vibration-detection thresholds (VDT), and pressure-pain thresholds (PPT) were determined at pain-related and control areas. Patients of the TG had significantly less pain after cupping therapy than patients of the WL group (PR: Δ-22.5 mm, p = 0.00002; PM: Δ-17.8 mm, p = 0.01). Pain diaries (PD) revealed that neck pain decreased gradually in the TG patients and that pain reported by the two groups differed significantly after the fifth cupping session (Δ-1.1, p = 0.001). There were also significant differences in the SF-36 subscales for bodily pain (Δ13.8, p = 0.006) and vitality (Δ10.2, p = 0.006). Group differences in PPT were significant at pain-related and control areas (all p < 0.05), but were not significant for MDT or VDT. A series of five dry cupping treatments appeared to be effective in relieving chronic non-specific neck pain. Not only subjective measures improved, but also mechanical pain sensitivity differed significantly between the two groups, suggesting that cupping has an influence on functional pain processing

The Effect of Traditional Cupping on Pain and Mechanical Thresholds in Patients with Chronic Nonspecific Neck Pain: A Randomised Controlled Pilot Study

Introduction. Cupping has been used since antiquity in the treatment of pain conditions. In this pilot study, we investigated the effect of traditional cupping therapy on chronic nonspecific neck pain (CNP) and mechanical sensory thresholds. Methods. Fifty CNP patients were randomly assigned to treatment (TG, n = 25) or waiting list control group (WL, n = 25). TG received a single cupping treatment. Pain at rest (PR), pain related to movement (PM), quality of life (SF-36), Neck Disability Index (NDI), mechanical detection (MDT), vibration detection (MDT), and pressure pain thresholds (PPT) were measured before and three days after a single cupping treatment. Patients also kept a pain and medication diary (PaDi, MeDi) during the study. Results. Baseline characteristics were similar in the two groups. After cupping TG reported significantly less pain (PR: −17.9 mm VAS, 95%CI −29.2 to −6.6; PM: −19.7, 95%CI −32.2 to −7.2; PaDi: −1.5 points on NRS, 95%CI −2.5 to −0.4; all P < 0.05) and higher quality of life than WL (SF-36, Physical Functioning: 7.5, 95%CI 1.4 to 13.5; Bodily Pain: 14.9, 95%CI 4.4 to 25.4; Physical Component Score: 5.0, 95%CI 1.4 to 8.5; all P < 0.05). No significant effect was found for NDI, MDT, or VDT, but TG showed significantly higher PPT at pain-areas than WL (in lg(kPa); pain-maximum: 0.088, 95%CI 0.029 to 0.148, pain-adjacent: 0.118, 95%CI 0.038 to 0.199; both P < 0.01). Conclusion. A single application of traditional cupping might be an effective treatment for improving pain, quality of life, and hyperalgesia in CNP