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Nijmegen, 22 januari 2008, Promotores : Falcke, H.D.E., Kuijpers, J.M.E. Co-promotores : Groot, P.J., Hörandel, J.R., Zarka, P., Contains fulltext : 72390.pdf (publisher's version ) (Open Access), This thesis consists of a detailed analysis of several observations with prototype stations of the Low Frequency Array (LOFAR). Chapter 1 introduces the field of radio astronomy, briefly describes the radio telescopes which were used and discusses radio frequency interference (RFI) and important tools for signal processing. Chapter 2 describes observations of Jupiter radio bursts, which were analyzed for propagation effects and cross-correlated with simultaneous observations of the Nançay Decametric Array. In Chapter 3, cosmic rays are introduced and the detection of radio emission from cosmic-ray air showers is described. The 4th chapter contains the description and discussion of radio spectra obtained from cosmic-ray air shower emission. In Chapter five, a technique to determine the directions of the measured radio emission from cosmic-ray events is discussed and compared to the directions provided by KASCADE. Some conclusions of the research results presented in this thesis are:- The source regions of Jupiter-Io S-bursts do not extend an angular size of 4 arcseconds.- Long baseline interferometry can be performed at low frequencies on periods from tens to hundreds of milliseconds with a baseline of about 700km, in spite of phase shifts introduced by variations in ionospheric propagation characteristics.- The electric field from high-energy cosmic-ray air showers has a steep spectrum decreasing in the LOPES band from 40MHz to 80MHz with a spectral index of -1.0, lying slightly above the slope obtained from Monte Carlo simulations based on air showers simulated with CORSIKA.- The directional accuracy of an interferometer, such as LOPES, was found to be strongly dependent on the curvature radius used for the near-field beam-forming.- Observations of events during thunderstorm activity confirmed theoretical predictions of a geoelectric effect.

Nijmegen, 19 december 2008, Promotores : Falcke, H.D.E., Kuijpers, J.M.E. Co-promotores : Jong, S.J. de, Hörandel, J.R., Huege, T., Contains fulltext : 72526.pdf (publisher's version ) (Open Access)

Contains fulltext : 70407.pdf (publisher's version ) (Open Access), BACKGROUND: Resistance to triazoles was recently reported in Aspergillus fumigatus isolates cultured from patients with invasive aspergillosis. The prevalence of azole resistance in A. fumigatus is unknown. We investigated the prevalence and spread of azole resistance using our culture collection that contained A. fumigatus isolates collected between 1994 and 2007. METHODS AND FINDINGS: We investigated the prevalence of itraconazole (ITZ) resistance in 1,912 clinical A. fumigatus isolates collected from 1,219 patients in our University Medical Centre over a 14-y period. The spread of resistance was investigated by analyzing 147 A. fumigatus isolates from 101 patients, from 28 other medical centres in The Netherlands and 317 isolates from six other countries. The isolates were characterized using phenotypic and molecular methods. The electronic patient files were used to determine the underlying conditions of the patients and the presence of invasive aspergillosis. ITZ-resistant isolates were found in 32 of 1,219 patients. All cases were observed after 1999 with an annual prevalence of 1.7% to 6%. The ITZ-resistant isolates also showed elevated minimum inhibitory concentrations of voriconazole, ravuconazole, and posaconazole. A substitution of leucine 98 for histidine in the cyp51A gene, together with two copies of a 34-bp sequence in tandem in the gene promoter (TR/L98H), was found to be the dominant resistance mechanism. Microsatellite analysis indicated that the ITZ-resistant isolates were genetically distinct but clustered. The ITZ-sensitive isolates were not more likely to be responsible for invasive aspergillosis than the ITZ-resistant isolates. ITZ resistance was found in isolates from 13 patients (12.8%) from nine other medical centres in The Netherlands, of which 69% harboured the TR/L98H substitution, and in six isolates originating from four other countries. CONCLUSIONS: Azole resistance has emerged in A. fumigatus and might be more prevalent than currentl

Contains fulltext : 65640.pdf ( ) (Open Access), LOPES is set up at the location of the KASCADE-Grande extensive air shower experiment in Karlsruhe, Germany and aims to measure and investigate radio pulses from Extensive Air Showers. Data taken during half a year of operation of 10 LOPES antennas (LOPES-10), triggered by showers observed with KASCADE-Grande have been analyzed. We report about results of correlations found of the measured radio signals by LOPES-10 with shower parameters.

Contains fulltext : 35150.pdf (preprint version ) (Open Access) Contains fulltext : 35150.pdf (publisher's version ) (Open Access), Context: The detection of radio pulses from cosmic ray air showers is a potentially powerful new detection mechanism for studying spectrum and composition of ultra high energy cosmic rays that needs to be understood in greater detail. The radiation consists in large part of geosynchrotron radiation. The intensity of this radiation depends, among other factors, on the energy of the primary particle and the angle of the shower axis with respect to the geomagnetic field. Aims: Since the radiation mechanism is based on particle acceleration, the atmospheric electric field can play an important role. Especially inside thunderclouds large electric fields can be present. In this paper we examine the contribution of an electric field to the emission mechanism theoretically and experimentally. Methods: Two mechanisms of amplification of radio emission are considered: the acceleration radiation of the shower particles and the radiation from the current that is produced by ionization electrons moving in the electric field. For both mechanisms analytical estimates are made of their effects on the radio pulse height. We selected lopes data recorded during thunderstorms, periods of heavy cloudiness and periods of cloudless weather. We tested whether the correlations with geomagnetic angle and primary energy vary with atmospheric conditions. Results: We find that during thunderstorms the radio emission can be strongly enhanced. The present data suggests that the observed amplification is caused by acceleration of the shower electrons and positrons. In the near future, extensions of lopes and the construction of lofar will help to identify the mechanism in more detail. No amplified pulses were found during periods of cloudless sky or heavy cloudiness, suggesting that the electric field effect for radio air shower measurements can be safely ignored during non-thunderstorm conditions.

Contains fulltext : 36666.pdf ( ) (Open Access) Contains fulltext : 36666.pdf (publisher's version ) (Open Access), Aims.To demonstrate and test the capability of the next generation of low-frequency radio telescopes to perform high resolution observations across intra-continental baselines. Jupiter's strong burst emission is used to perform broadband full signal cross-correlations on time intervals of up to hundreds of milliseconds. Methods: Broadband VLBI observations at about 20 MHz on a baseline of ~50 000 wavelengths were performed to achieve arcsecond angular resolution. lofar's Initial Test Station (lofar/its, The Netherlands) and the Nançay Decametric Array (nda, France) digitize the measured electric field with 12 bit and 14 bit in a 40 MHz baseband. The fine structure in Jupiter's signal was used for data synchronization prior to correlation on the time-series data. Results : Strong emission from Jupiter was detected during snapshots of a few seconds and detailed features down to microsecond time-scales were identified in dynamic spectra. Correlations of Jupiter's burst emission returned strong fringes on 1 ms time-scales over channels as narrow as a hundred kilohertz bandwidth. Conclusions: Long baseline interferometry is confirmed at low frequencies, in spite of phase shifts introduced by variations in ionospheric propagation characteristics. Phase coherence was preserved over tens to hundreds of milliseconds with a baseline of ~700 km. No significant variation with time was found in the correlations and an estimate for the fringe visibility of 1, suggested that the source was not resolved. The upper limit on the source region size of Jupiter Io-B S-bursts corresponds to an angular resolution of ~3 arcsec. Adding remote stations to the lofar network at baselines up to thousand kilometers will provide 10 times higher resolution down to an arcsecond.

Contains fulltext : 36387.pdf ( ) (Open Access) Contains fulltext : 36387.pdf (publisher's version ) (Open Access), Aims.The capability of radio antenna arrays to measure cosmic ray air showers with very large zenith angles is explored. This is important, since a possible neutrino detection has to fulfill two requirements. First: antennas should be able to detect very inclined cosmic ray air showers, and second: it should be possible to estimate the distance to the shower maximum, since neutrinos are most likely to travel far through the Earth's atmosphere without interaction and induce air showers close to the ground. Methods: LOPES (LOFAR PrototypE Station; LOFAR - LOw Frequency ARray), an array of dipole antennas, is used for the detection of inclined cosmic ray air showers. LOPES is co-located and triggered by the KASCADE (KArlsruhe Shower Core and Array DEtector) experiment, which also provides information on air shower properties such as electron and muon numbers on the ground, as well as the arrival direction. Radio emission of nearly vertical cosmic ray air showers has been detected by LOPES. Results: LOPES-10 (the first phase of LOPES, consisting of 10 antennas) detected a significant number of cosmic ray air showers with a zenith angle larger than 50°, and many of these have very high radio field strengths. The most inclined event that has been detected with LOPES-10 has a zenith angle of almost 80°. This is proof that the new technique is also applicable for cosmic ray air showers with high inclinations, which in the case that they are initiated close to the ground, can be a signature of neutrino events. Conclusions: .Our results indicate that arrays of simple radio antennas can be used for the detection of highly inclined air showers, which might be triggered by neutrinos. In addition, we found that the radio pulse height (normalized with the muon number) for highly inclined events increases with the geomagnetic angle, which confirms the geomagnetic origin of radio emission in cosmic ray air showers.

Contains fulltext : 36588.pdf ( ) (Open Access) Contains fulltext : 36588.pdf (publisher's version ) (Open Access), Context: PSR B0031-07 is well known to exhibit three different modes of drifting sub-pulses (mode A, B and C). It has recently been shown that in a multifrequency observation, consisting of 2700 pulses, all driftmodes were visible at low frequencies, while at 4.85 GHz only mode-A drift or non-drifting emission was detected. This suggests that modes A and B are emitted in sub-beams, rotating at a fixed distance from the magnetic axis, with the mode-B sub-beams being closer to the magnetic axis than the mode-A sub-beams. Diffuse emission between the sub-beams can account for the non-drifting emission. Aims: Using the results of an analysis of simultaneous multifrequency observations of PSR B0031-07, we set out to construct a geometrical model that includes emission from both sub-beams and diffuse emission and describes the regions of the radio emission of PSR B0031-07 at each emission frequency for driftmodes A and B. Methods: Based on the vertical spacing between driftbands, we have determined the driftmode of each sequence of drift. To restrict the model, we calculated average polarisation and intensity characteristics for each driftmode and at each frequency. Results: The model reproduces the observed polarisation and intensity characteristics, suggesting that diffuse emission plays an important role in the emission properties of PSR B0031-07. The model further suggests that the emission heights of this pulsar range from a few kilometers to a little over 10 kilometers above the pulsar surface. We also find that the relationships between height and frequency of emission that follow from curvature radiation and from plasma-frequency emission could not be used to reproduce the observed frequency dependence of the width of the average intensity profiles.

Contains fulltext : 36384.pdf ( ) (Open Access), When Ultra High Energy Cosmic Rays (UHECR) interact with particles in the Earth's atmosphere, they produce a shower of secondary particles propagating toward the ground. LOPES-30 is an absolutely calibrated array of 30 dipole antennas investigating the radio emission from these showers in detail and clarifying if the technique is useful for large-scale applications. LOPES-30 is co-located and measures in coincidence with the air shower experiment KASCADE-Grande. Status of LOPES-30 and first measurements are presented.

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Contains fulltext : 35465.pdf (preprint version ) (Open Access), The origin of high-energy cosmic rays in the energy range from 1014 to 1018 eV is explored with the KASCADE and KASCADE-Grande experiments. Radio signals from air showers are measured with the LOPES experiment. An overview on results is given.

Contains fulltext : 36135.pdf (publisher's version ) (Closed access), The LOPES experiment (LOfar Prototype Station) has been built at the KASCADE-Grande experiment in order to test the LOFAR (LOw Frequency ARray) technology and demonstrate its capability for radio measurements in Extensive Air Showers (EAS). After the first positive results in the framework of the KASCADE-Grande experiment we developed the next generation of antennas, electronics, and trigger. The main new features are easy calibration of antennas with precise detection of polarization, and good capability of self-triggering. The results from this new design are under test in Karlsruhe. Furthermore the background situation was measured and analyzed.

Contains fulltext : 35498.pdf (publisher's version ) (Closed access), Measuring radio pulses from cosmic ray air showers offers various new opportunities. New digital radio receivers allow measurements of these radio pulses even in environments that have lots of radio interference. With high bandwidth ADCs and fast data processing it is possible to store the whole waveform information in digital form and analyse transient events like air showers even after they have been recorded. Digital filtering and beam forming can be used to suppress the radio interference so that it is possible to measure the radio pulses even in radio loud environments. LOPES is a prototype station for the new digital radio interferometer LOFAR and is tailored to measure air showers. For this it is located at the site of the KASCADE-Grande air shower experiment. Already with the first phase of LOPES we have been able to measure radio pulses from air showers and show correlations between the radio pulse height and air shower parameters. The first part gives an introduction and presents the science results of LOPES, while the second part presents the hard- and software that enables LOPES to detect air short pulses.

Contains fulltext : 35501.pdf (publisher's version ) (Open Access), The potential role of a diocotron instability in causing drifting sub-pulses in radio pulsar emission is investigated for aligned magnetic rotators. It is assumed that the out-flowing plasma above a pulsar polar cap consists of an initially axially symmetric, hollow beam of relativistic electron positron pair plasma which carries an electric charge as well as a current. The occurrence of instability depends on shear in the angular velocity distribution of the beam as a function of axial distance. Instability occurs under typical pulsar conditions at mode numbers ≤ 40. It destroys the symmetry of the equilibrium configuration and leads to a carousel of density columns which rotates at fixed angular pattern speed. The process is applied to two pulsars with observed carousels of drifting sub-pulses, and the diocotron instability at corresponding mode number and axial distance is used as a diagnostic for the charge and current density of the polar flow.

Contains fulltext : 35419.pdf ( ) (Open Access), Gravitational waves (GW) propagating through a magnetized plasma excite low-frequency magnetohydrodynamic (MHD) waves. In this paper, we investigate whether these waves can produce observable radio emission at higher frequencies by scattering on an anisotropic intrinsically relativistic distribution of electrons and positrons in the force-free wind surrounding a double neutron star binary merger. The relativistic particle distribution is assumed to be strictly along the magnetic field lines, while the magneto-plasma streams out at a relativistic speed from the neutron stars. In the case of Compton scattering of an incident MHD wave transverse to the magnetic field, we find that the probability of scattering to both a transverse x-mode and a quasi-longitudinal Langmuir-ordinary mode is suppressed when the frequency of the incident wave is below the local relativistic gyro-frequency, that is, when the magnetic field is very strong.

Nijmegen, 08 mei 2006, Promotor : Kuijpers, J.M.E., Contains fulltext : 27430.pdf (publisher's version ) (Open Access), In this thesis I discuss the importance of general relativity on plasma physics in several astrophysical and cosmological contexts. The first chapters show how gravitational waves can excite all three fundamental low frequency magnetohydrodynamic plasma modes, the Alfven, slow and fast magnetoacousic waves. Then, in a predominantly special relativistic context the inverse Compton scattering of these low frequency waves to radio waves is studied, which could make gravitational waves indirectly detectable with the Dutch LOw Frequency Array (LOFAR). As a cosmological application of general relativistic plasma dynamics, I consider scalar perturbations on a two-temperature plasma filling the entire Universe

Contains fulltext : 35479.pdf ( ) (Open Access), Data taken during half a year of operation of 10 LOPES antennas (LOPES-10), triggered by EAS observed with KASCADE-Grande have been analysed. We report about the analysis of correlations of radio signals measured by LOPES-10 with extensive air shower events reconstructed by KASCADE-Grande, including shower cores at large distances. The efficiency of detecting radio signals induced by air showers up to distances of 700 m from the shower axis has been investigated. The results are discussed with special emphasis on the effects of the reconstruction accuracy for shower core and arrival direction on the coherence of the measured radio signal. In addition, the correlations of the radio pulse amplitude with the primary cosmic ray energy and with the lateral distance from the shower core are studied.

Contains fulltext : 36122.pdf (preprint version ) (Open Access), Radio emission in extensive air showers arises from an interaction with the geomagnetic field and is subject of theoretical studies. This radio emission has advantages for the detection of high energy cosmic rays compared to secondary particle or fluorescence measurement methods. Radio antennas like the LOPES30 antenna system are suited to investigate this emission process by detecting the radio pulses. The characteristic observable parameters like electric field strength and pulse length require a calibration which was done with a reference radio source resulting in an amplification factor representing the system behavior in the environment of the KASCADE-Grande experiment. Knowing the amplification factor and the gain of the LOPES antennas LOPES30 is calibrated absolutely for systematic analyses of the radio emission.

Contains fulltext : 36004.pdf (preprint version ) (Open Access), First analyses of coincident data of the LOPES (LOfar PrototypE Station) radio antennas with the particle air shower experiment KASCADE-Grande show basic correlations in the observed shower parameters, like the strength of the radio signal and the particle number, or comparing the estimated shower directions. In addition, an improvement of the experimental resolution of the shower parameters reconstructed by KASCADE-Grande can be obtained by including the data of the radio antennas. This important feature will be shown in this article explicitely by an example event.

Contains fulltext : 35515.pdf (publisher's version ) (Open Access), Genomes and antigenomes of many positive-strand RNA viruses contain 3'-poly(A) and 5'-poly(U) tracts, respectively, serving as mutual templates. Mechanism(s) controlling the length of these homopolymeric stretches are not well understood. Here, we show that in coxsackievirus B3 (CVB3) and three other enteroviruses the poly(A) tract is approximately 80-90 and the poly(U) tract is approximately 20 nt-long. Mutagenesis analysis indicate that the length of the CVB3 3'-poly(A) is determined by the oriR, a cis-element in the 3'-noncoding region of viral RNA. In contrast, while mutations of the oriR inhibit initiation of (-) RNA synthesis, they do not affect the 5'-poly(U) length. Poly(A)-lacking genomes are able to acquire genetically unstable AU-rich poly(A)-terminated 3'-tails, which may be generated by a mechanism distinct from the cognate viral RNA polyadenylation. The aberrant tails ensure only inefficient replication. The possibility of RNA replication independent of oriR and poly(A) demonstrate that highly debilitated viruses are able to survive by utilizing 'emergence', perhaps atavistic, mechanisms.

Nijmegen, The Netherlands, 24 oktober 2006, Promotor : Kuijpers, J.M.E. Co-promotor : Stappers, B.W., Contains fulltext : 36190.pdf (publisher's version ) (Open Access), This thesis consists of a number of studies on the radio emission of pulsars. The central topics are polarisation and multi frequency observations, which both lead to important information on the geometry of the emission. The first chapter introduces different aspects of pulsars that are related to the research that has been done in this thesis. In particular it deals with different aspects concerning the geometry of pulsar emission. Chapter 2 is about the nature of the radio emission. It shows the result of an attempt to confirm and expand on work that has been published by Jenet et al. (2001) on the detection of coherence in pulsar radiation. From an analysis of high time resolution observations, we found that the detection of coherence is consistent with the effects of interstellar scintillation. In chapter 3 a study is carried out on the orthogonal polarisation mode behaviour as a function of frequency of 18 pulsars. By making the assumption that the radiation consists of two 100% polarised completely orthogonal superposed modes, both modes could be separated In chapter 4 PSR B0031-07 is studied at two frequencies using two observations that were carried out simultaneously. It is shown that from the three known drift modes, only one drift mode is seen at high frequency. Based on this result we suggest a geometrical model in which different modes are emitted in concentric rings around the magnetic axis, with each mode having a different radius. The fifth chapter follows the suggestions made in chapter 4 to create a geometrical model of PSR B0031-07 for two of the drift modes. The results can be used to limit the possible geometries of PSR B0031-07. The final chapter consists of documentation of software that was written in C and utilised for this thesis for handling and analysing data files in the EPN format