A Method to Polarize Stored Antiprotons to a High Degree

Polarized antiprotons can be produced in a storage ring by spin--dependent interaction in a purely electron--polarized hydrogen gas target. The polarizing process is based on spin transfer from the polarized electrons of the target atoms to the orbiting antiprotons. After spin filtering for about two beam lifetimes at energies $T\approx 40-170$ MeV using a dedicated large acceptance ring, the antiproton beam polarization would reach $P=0.2-0.4$. Polarized antiprotons would open new and unique research opportunities for spin--physics experiments in $\bar{p}p$ interactions

J Theor Biol

One of the most important antioxidant enzymes is superoxide dismutase (SOD), which catalyses the dismutation of superoxide radicals to hydrogen peroxide. The enzyme plays an important role in diseases like trisomy 21 and also in theories of the mechanisms of aging. But instead of being beneficial, intensified oxidative stress is associated with the increased expression of SOD and also studies on bacteria and transgenic animals show that high levels of SOD actually lead to increased lipid peroxidation and hypersensitivity to oxidative stress. Using mathematical models we investigate the question how overexpression of SOD can lead to increased oxidative stress, although it is an antioxidant enzyme. We consider the following possibilities that have been proposed in the literature: (i) Reaction of H2O2 with CuZnSOD leading to hydroxyl radical formation. (ii) Superoxide radicals might reduce membrane damage by acting as radical chain breaker. (iii) While detoxifying superoxide radicals SOD cycles between a reduced and oxidized state. At low superoxide levels the intermediates might interact with other redox partners and increase the superoxide reductase (SOR) activity of SOD. This short-circuiting of the SOD cycle could lead to an increased hydrogen peroxide production. We find that only one of the proposed mechanisms is under certain circumstances able to explain the increased oxidative stress caused by SOD. But furthermore we identified an additional mechanism that is of more general nature and might be a common basis for the experimental findings. We call it the alternative pathway mechanism

Beam Performance and Luminosity Limitations in the High-Energy Storage Ring (HESR)

The High-Energy Storage Ring (HESR) of the future International Facility for Antiproton and Ion Research (FAIR) at GSI in Darmstadt is planned as an antiproton synchrotron and storage ring in the momentum range from 1.5 to 15 GeV/c. An important feature of this new facility is the combination of phase space cooled beams with dense internal targets (e.g. pellet targets), resulting in demanding beam parameter of two operation modes: high luminosity mode with peak luminosities up to 2*10^32 cm-2 s-1, and high resolution mode with a momentum spread down to 10^-5, respectively. To reach these beam parameters very powerful phase space cooling is needed, utilizing high-energy electron cooling and high-bandwidth stochastic cooling. The effect of beam-target scattering and intra-beam interaction is investigated in order to study beam equilibria and beam losses for the two different operation modes.Comment: 8 pages, based on a talk presented at COULOMB'05, Accepted for publication by Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipmen

Creation and application of immortalized bait libraries for targeted enrichment and next-generation sequencing

Since the introduction of next-generation sequencing, several techniques have been developed to selectively enrich and sequence specific parts of the genome at high coverage. These techniques include enzymatic methods employing molecular inversion probes, PCR based approaches, hybrid capture, and in-solution capture. In-solution capture employs RNA probes transcribed from a pool of DNA template oligos designed to match regions of interest to specifically bind and enrich genomic DNA fragments. This method is highly efficient, especially if genomic target regions are large in size or quantity. Diverse in-solution capture kits are available, but are costly when large sample numbers need to be analyzed. Here we present a cost-effective strategy for the design of custom DNA libraries, their transcription into RNA libraries, and application for in-solution capture. We show the efficacy by comparing the method to a commercial kit and further demonstrate that emulsion PCR can be used for bias free amplification and virtual immortalization of DNA template libraries

A recoil detector for the measurement of antiproton-proton elastic scattering at angles close to 90∘^{\circ}

The design and construction of a recoil detector for the measurement of recoil protons of antiproton-proton elastic scattering at scattering angles close to 90$^{\circ}$ are described. The performance of the recoil detector has been tested in the laboratory with radioactive sources and at COSY with proton beams by measuring proton-proton elastic scattering. The results of laboratory tests and commissioning with beam are presented. Excellent energy resolution and proper working performance of the recoil detector validate the conceptual design of the KOALA experiment at HESR to provide the cross section data needed to achieve a precise luminosity determination at the PANDA experiment.Comment: 10 pages, 15 figure

IT Future of Medicine: from molecular analysis to clinical diagnosis and improved treatment

The IT Future of Medicine (ITFoM, http://www.itfom.eu/) initiative will produce computational models of individuals to enable the prediction of their future health risks, progression of diseases and selection and efficacy of treatments while minimising side effects. To be able to move our health care system to treat patients as individuals rather than as members of larger, divergent groups, the ITFoM initiative, proposes to integrate molecular, physiological and anatomical data of every person in 'virtual patient' models. The establishment of such 'virtual patient' models is now possible due to the enormous progress in analytical techniques, particularly in the '-omics' technology areas and in imaging, as well as in sensor technologies, but also due to the immense developments in the ICT field. As one of six Future and Emerging Technologies (FET) Flagship Pilot Projects funded by the European Commission, ITFoM with more than 150 academic and industrial partners from 34 countries, will foster the development in functional genomics and computer technologies to generate 'virtual patient' models to make them available for clinical application. The increase in the capacity of next generation sequencing systems will enable the high-throughput analysis of a large number of individuals generating huge amounts of genome, epigenome and transcriptome data, but making it feasible to apply deep sequencing in the clinic to characterise not only the patient's genome, but also individual samples, for example, from tumours. The genome profile will be integrated with proteome and metabolome information generated via new powerful chromatography, mass spectrometry and nuclear magnetic resonance techniques. The individualised model will not only enable the analysis of the current situation, but will allow the prediction of the response of the patient to different therapy options or intolerance for certain drugs

In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system

In the postgenomic era many experiments rely on the availability of transcript sequence for cloning. As these clones usually originate from cDNA libraries, the quality of these libraries is crucial. If a good library is generated it is desirable to use a versatile cloning system suitable for many different kinds of applications. The cloning systems based on in vitro recombination proves fitting for this task. However, the use of this method for shuttling entire cDNA libraries between different vectors has not yet been studied in great detail. Here we describe the construction of four cDNA libraries from different tissues of Arabidopsis thaliana, the shuttling of the libraries into expression vectors, and evaluation of this method as well as its suitability for downstream applications. Libraries were constructed from seedlings, hormone treated seedlings, flowers, developing seeds and primary leaves in the ldquoentry vectorrdquo of the Gatewaytrade cloning system. After initial characterization of the libraries, they were shuttled into an expression vector (a yeast two-hybrid prey vector). To monitor for a size bias generally assumed to be inherent to in vitro recombination methods, the libraries were characterized before and after the transfer into the expression vector. However no significant difference could be detected. The functionality of the in vitro recombination system for the shuttling of entire libraries was then further tested by protein-protein interaction screens. The results of the library characterization and of the yeast two-hybrid screens and their implications for large-scale proteomic approaches are discussed

Polarized Proton Beams from Laser-induced Plasmas

We report on the concept of an innovative source to produce polarized proton/deuteron beams of a kinetic energy up to several GeV from a laser-driven plasma accelerator. Spin effects have been implemented into the PIC simulation code VLPL to make theoretical predictions about the behavior of proton spins in laser-induced plasmas. Simulations of spin-polarized targets show that the polarization is conserved during the acceleration process. For the experimental realization, a polarized HCl gas-jet target is under construction using the fundamental wavelength of a Nd:YAG laser system to align the HCl bonds and simultaneously circular polarized light of the fifth harmonic to photo-dissociate, yielding nuclear polarized H atoms. Subsequently, their degree of polarization is measured with a Lamb-shift polarimeter. The final experiments, aiming at the first observation of a polarized particle beam from laser-generated plasmas, will be carried out at the 10 PW laser system SULF at SIOM/Shanghai.Comment: 7 pages, 7 figure

Electromagnetic Simulation and Design of a Novel Waveguide RF Wien Filter for Electric Dipole Moment Measurements of Protons and Deuterons

The conventional Wien filter is a device with orthogonal static magnetic and electric fields, often used for velocity separation of charged particles. Here we describe the electromagnetic design calculations for a novel waveguide RF Wien filter that will be employed to solely manipulate the spins of protons or deuterons at frequencies of about 0.1 to 2 MHz at the COoler SYnchrotron COSY at J\"ulich. The device will be used in a future experiment that aims at measuring the proton and deuteron electric dipole moments, which are expected to be very small. Their determination, however, would have a huge impact on our understanding of the universe.Comment: 10 pages, 10 figures, 4 table

Distinguishing regional from within-codon rate heterogeneity in DNA sequence alignments

We present an improved phylogenetic factorial hidden Markov model (FHMM) for detecting two types of mosaic structures in DNA sequence alignments, related to (1) recombination and (2) rate heterogeneity. The focus of the present work is on improving the modelling of the latter aspect. Earlier papers have modelled different degrees of rate heterogeneity with separate hidden states of the FHMM. This approach fails to appreciate the intrinsic difference between two types of rate heterogeneity: long-range regional effects, which are potentially related to differences in the selective pressure, and the short-term periodic patterns within the codons, which merely capture the signature of the genetic code. We propose an improved model that explicitly distinguishes between these two effects, and we assess its performance on a set of simulated DNA sequence alignments