Software tools and efficient algorithms for the feature detection, feature tracking, event localization, and visualization of large sets of atmospheric data

Data sets describing the state of the earth's atmosphere are of great importance in the atmospheric sciences. Over the last decades, the quality and sheer amount of the available data increased significantly, resulting in a rising demand for new tools capable of handling and analysing these large, multidimensional sets of atmospheric data. The interdisciplinary work presented in this thesis covers the development and the application of practical software tools and efficient algorithms from the field of computer science, aiming at the goal of enabling atmospheric scientists to analyse and to gain new insights from these large data sets. For this purpose, our tools combine novel techniques with well-established methods from different areas such as scientific visualization and data segmentation. In this thesis, three practical tools are presented. Two of these tools are software systems (Insight and IWAL) for different types of processing and interactive visualization of data, the third tool is an efficient algorithm for data segmentation implemented as part of Insight.Insight is a toolkit for the interactive, three-dimensional visualization and processing of large sets of atmospheric data, originally developed as a testing environment for the novel segmentation algorithm. It provides a dynamic system for combining at runtime data from different sources, a variety of different data processing algorithms, and several visualization techniques. Its modular architecture and flexible scripting support led to additional applications of the software, from which two examples are presented: the usage of Insight as a WMS (web map service) server, and the automatic production of a sequence of images for the visualization of cyclone simulations. The core application of Insight is the provision of the novel segmentation algorithm for the efficient detection and tracking of 3D features in large sets of atmospheric data, as well as for the precise localization of the occurring genesis, lysis, merging and splitting events. Data segmentation usually leads to a significant reduction of the size of the considered data. This enables a practical visualization of the data, statistical analyses of the features and their events, and the manual or automatic detection of interesting situations for subsequent detailed investigation. The concepts of the novel algorithm, its technical realization, and several extensions for avoiding under- and over-segmentation are discussed. As example applications, this thesis covers the setup and the results of the segmentation of upper-tropospheric jet streams and cyclones as full 3D objects. Finally, IWAL is presented, which is a web application for providing an easy interactive access to meteorological data visualizations, primarily aimed at students. As a web application, the needs to retrieve all input data sets and to install and handle complex visualization tools on a local machine are avoided. The main challenge in the provision of customizable visualizations to large numbers of simultaneous users was to find an acceptable trade-off between the available visualization options and the performance of the application. Besides the implementational details, benchmarks and the results of a user survey are presented.

A single chain antibody against a viral RNA polymerase (TBSV-BS3-Statice)

Expression of antibodies in plant against essential viral proteins could provide an alternative approach to engineered viral resistance. Engineered single chain Fv antibodies scFV are particularly suitable for expression in plant because of their small size and the lack of assembly requirements. RNA-dependent RNA polymerases (RdRps) function as the catalytic subunit of viral replicases required for the replication of all positive strand RNA viruses. By using Phage technology we selected scFvs from a phage library using purified E.coli expressed TBSV(Tomato bushy stunt virus) replicase as antigen. The scFvs mediated-inhibition of RdRp activity was studied in vitro and in planta. In vitro experiments showed the inhibition of CNV(Cucumber necrosis virus) and TCV(Turnip crinkle virus) RdRp. Transient in planta assays based on agroinfiltration and an infectious clone of TBSV demonstrated the inhibition of the replication of TBSV(Tomato bushy stunt virus). Epitope mapping showed that the selected scFvs target the motif E of RdRp which is involved in template binding.Moreover T1 plants of transgenic lines of N. benthamiana expressing different scFvs either in the cytoplasm or the ER (endoplasmic reticulum) showed a high level of resistance against infection with TBSV and RCNMV(Red clover necrotic mosaic virus) upon inoculation with virus particles. This is the first report that scFvs against a RdRp of a plant viruses can inhibit viral replication in vivo. The resistance is even efficient against viruses belonging to different virus families.

Funktionelle Magnetresonanztomographie mittels simultaner EEG-Registrierung interiktaler Spikes bei fokaler Epilepsie: Vergleich der on-, off- mit der häufigkeitskorrelierten Datenanalyse

Obwohl die funktionelle Magnetresonanztomographie (fMRI) interiktaler Spikes mit simultaner EEG-Ableitung bei Patienten mit fokalen Anfallsleiden seit einigen Jahren zur Lokalisation beteiligter Hirnstrukturen untersucht wird, ist sie nach wie vor eine experimentelle Methode. Um zuverlässig Ergebnisse zu erhalten, ist insbesondere die Verbesserung des Signal-zu-Rausch-Verhältnisses in der statistischen Bilddatenauswertung von Bedeutung. Frühere Untersuchungen zur sog. event-related fMRI weisen auf einen Zusammenhang zwischen Häufigkeit von Einzelreizen und nachfolgender hämodynamischer Signalantwort in der fMRI hin. Um einen möglichen Einfluss der Häufigkeit interiktaler Spikes auf die Signalantwort nachzuweisen, wurden 20 Kinder mit fokaler Epilepsie mit der EEG-fMRI untersucht. Von 11 dieser Patienten konnten die Daten ausgewertet werden. In einer zweifachen Analyse mit dem Softwarepaket SPM99 wurden die Bilddaten zuerst ausschließlich je nach Auftreten interiktaler Spikes der „Reiz“- oder „Ruhe“-Bedingung zugeordnet, unabhängig von der jeweiligen Anzahl der Spikes je Messzeitpunkt (on/off-Analyse). In einem zweiten Schritt wurden die „Reiz“- Bedingungen auch differenziert nach jeweiliger Anzahl einzelner Spikes ausgewertet (häufigkeitskorrelierte Analyse). Die Ergebnisse dieser Analysen zeigten bei 5 der 11 Patienten eine Zunahme von Sensitivität und Signifikanzen der in der fMRI nachgewiesenen Aktivierungen. Eine höhere Spezifität konnte hingegen nicht gezeigt werden. Diese Ergebnisse weisen auf eine positive Korrelation von Reizhäufigkeit und nachfolgender hämodynamischer Antwort auch bei interiktalen Spikes hin, welche für die EEG-fMRI nutzbar ist. Bei 6 Patienten konnte keine fMRI-Aktivierung nachgewiesen werden. Mögliche technische und physiologische Ursachen hierfür werden diskutiert.

A new double laser pulse pumping scheme for transient collisionally excited plasma soft X-ray lasers

Within this thesis a new double laser pulse pumping scheme for plasma-based, transient collisionally excited soft x-ray lasers (SXRL) was developed, characterized and utilized for applications. SXRL operations from ~50 up to ~200 electron volt were demonstrated applying this concept. As a central technical tool, a special Mach-Zehnder interferometer in the chirped pulse amplification (CPA) laser front-end was developed for the generation of fully controllable double-pulses to optimally pump SXRLs.rnThis Mach-Zehnder device is fully controllable and enables the creation of two CPA pulses of different pulse duration and variable energy balance with an adjustable time delay. Besides the SXRL pumping, the double-pulse configuration was applied to determine the B-integral in the CPA laser system by amplifying short pulse replica in the system, followed by an analysis in the time domain. The measurement of B-integral values in the 0.1 to 1.5 radian range, only limited by the reachable laser parameters, proved to be a promising tool to characterize nonlinear effects in the CPA laser systems.rnContributing to the issue of SXRL pumping, the double-pulse was configured to optimally produce the gain medium of the SXRL amplification. The focusing geometry of the two collinear pulses under the same grazing incidence angle on the target, significantly improved the generation of the active plasma medium. On one hand the effect was induced by the intrinsically guaranteed exact overlap of the two pulses on the target, and on the other hand by the grazing incidence pre-pulse plasma generation, which allows for a SXRL operation at higher electron densities, enabling higher gain in longer wavelength SXRLs and higher efficiency at shorter wavelength SXRLs. The observation of gain enhancement was confirmed by plasma hydrodynamic simulations.rnThe first introduction of double short-pulse single-beam grazing incidence pumping for SXRL pumping below 20 nanometer at the laser facility PHELIX in Darmstadt (Germany), resulted in a reliable operation of a nickel-like palladium SXRL at 14.7 nanometer with a pump energy threshold strongly reduced to less than 500 millijoule. With the adaptation of the concept, namely double-pulse single-beam grazing incidence pumping (DGRIP) and the transfer of this technology to the laser facility LASERIX in Palaiseau (France), improved efficiency and stability of table-top high-repetition soft x-ray lasers in the wavelength region below 20 nanometer was demonstrated. With a total pump laser energy below 1 joule the target, 2 mircojoule of nickel-like molybdenum soft x-ray laser emission at 18.9 nanometer was obtained at 10 hertz repetition rate, proving the attractiveness for high average power operation. An easy and rapid alignment procedure fulfilled the requirements for a sophisticated installation, and the highly stable output satisfied the need for a reliable strong SXRL source. The qualities of the DGRIP scheme were confirmed in an irradiation operation on user samples with over 50.000 shots corresponding to a deposited energy of ~ 50 millijoule.rnThe generation of double-pulses with high energies up to ~120 joule enabled the transfer to shorter wavelength SXRL operation at the laser facility PHELIX. The application of DGRIP proved to be a simple and efficient method for the generation of soft x-ray lasers below 10 nanometer. Nickel-like samarium soft x-ray lasing at 7.3 nanometer was achieved at a low total pump energy threshold of 36 joule, which confirmed the suitability of the applied pumping scheme. A reliable and stable SXRL operation was demonstrated, due to the single-beam pumping geometry despite the large optical apertures. The soft x-ray lasing of nickel-like samarium was an important milestone for the feasibility of applying the pumping scheme also for higher pumping pulse energies, which are necessary to obtain soft x-ray laser wavelengths in the water window. The reduction of the total pump energy below 40 joule for 7.3 nanometer short wavelength lasing now fulfilled the requirement for the installation at the high-repetition rate operation laser facility LASERIX.rn

Fluctuation spectroscopy of single plasmonic nanostructures

Plasmonic nanoparticles are great candidates for sensing applications with optical read-out. Plasmon sensing is based on the interaction of the nanoparticle with electromagnetic waves where the particle scatters light at its resonance wavelength. This wavelength depends on several intrinsic factors like material, shape and size of the nanoparticle as well as extrinsic factors like the refractive index of the surrounding medium. The latter allows the nanoparticle to be used as a sensor; changes in the proximate environment can be directly monitored by the wavelength of the emitted light. Due to their minuscule size and high sensitivity this allows individual nanoparticles to report on changes in particle coverage.rnrnTo use this single particle plasmon sensor for future sensing applications it has to meet the demand for detection of incidents on the single molecule level, such as single molecule sensing or even the detection of conformational changes of a single molecule. Therefore, time resolution and sensitivity have to be enhanced as today’s measurement methods for signal read-out are too slow and not sensitive enough to resolve these processes. This thesis presents a new experimental setup, the 'Plasmon Fluctuation Setup', that leads to tremendous improvements in time resolution and sensitivity. This is achieved by implementation of a stronger light source and a more sensitive detector. The new setup has a time resolution in the microsecond regime, an advancement of 4-6 orders of magnitude to previous setups. Its resonance wavelength stability of 0.03 nm, measured with an exposure time of 10 ms, is an improvement of a factor of 20 even though the exposure time is 3000 times shorter than in previous reports. Thus, previously unresolvable wavelength changes of the plasmon sensor induced by minor local environmental alteration can be monitored with extremely high temporal resolution.rnrnUsing the 'Plasmon Fluctuation Setup', I can resolve adsorption events of single unlabeled proteins on an individual nanorod. Additionally, I monitored the dynamic evolution of a single protein binding event on a millisecond time scale. This feasibility is of high interest as the role of certain domains in the protein can be probed by a study of modified analytes without the need for labels possibly introducing conformational or characteristic changes to the target. The technique also resolves equilibrium fluctuations in the coverage, opening a window into observing Brownian dynamics of unlabeled macromolecules. rnrnA further topic addressed in this thesis is the usability of the nanoruler, two nanospheres connected with a spacer molecule, as a stiffness sensor for the interparticle linker under strong illumination. Here, I discover a light induced collapse of the nanoruler. Furthermore, I exploit the sensing volume of a fixed nanorod to study unlabeled analytes diffusing around the nanorod at concentrations that are too high for fluorescence correlation spectroscopy but realistic for biological systems. Additionally, local pH sensing with nanoparticles is achieved.

Consequences of DNA damage for gene transcription : direct effects of modified nucleobases and the role of base excision repair = Folgen von DNA-Schäden für die Gentranskription

The presence of damaged nucleobases in DNA can negatively influence transcription of genes. One of the mechanisms by which DNA damage interferes with reading of genetic information is a direct blockage of the elongating RNA polymerase complexes – an effect well described for bulky adducts induced by several chemical substances and UV-irradiation. However, other mechanisms must exist as well because many of the endogenously occurring non-bulky DNA base modifications have transcription-inhibitory properties in cells, whilstrnnot constituting a roadblock for RNA polymerases under cell free conditions. The inhibition of transcription by non-blocking DNA damage was investigated in this work by employing the reporter gene-based assays. Comparison between various types of DNA damage (UV-induced pyrimidine photoproducts, oxidative purine modifications induced by photosensitisation, defined synthetic modified bases such as 8-oxoguanine and uracil, and sequence-specific single-strand breaks) showed that distinct mechanisms of inhibition of transcription can be engaged, and that DNA repair can influence transcription of the affectedrngenes in several different ways.rnQuantitative expression analyses of reporter genes damaged either by the exposure of cells to UV or delivered into cells by transient transfection supported the earlier evidence that transcription arrest at the damage sites is the major mechanism for the inhibition of transcription by this kind of DNA lesions and that recovery of transcription requires a functional nucleotide excision repair gene Csb (ERCC6) in mouse cells. In contrast, oxidisedrnpurines generated by photosensitisation do not cause transcriptional blockage by a direct mechanism, but rather lead to transcriptional repression of the damaged gene which is associated with altered histone acetylation in the promoter region. The whole chain of events leading to transcriptional silencing in response to DNA damage remains to be uncovered. Yet, the data presented here identify repair-induced single-strand breaks – which arise from excision of damaged bases by the DNA repair glycosylases or endonucleases – as arnputative initiatory factor in this process. Such an indirect mechanism was supported by requirement of the 8-oxoguanine DNA glycosylase (OGG1) for the inhibition of transcription by synthetic 8-oxodG incorporated into a reporter gene and by the delays observed for the inhibition of transcription caused by structurally unrelated base modifications (8-oxoguanine and uracil). It is thereby hypothesized that excision of the modified bases could be a generalrnmechanism for inhibition of transcription by DNA damage which is processed by the base excision repair (BER) pathway. Further gene expression analyses of plasmids containing single-strand breaks or abasic sites in the transcribed sequences revealed strong transcription inhibitory potentials of these lesions, in agreement with the presumption that BER intermediates are largely responsible for the observed effects. Experiments with synthetic base modifications positioned within the defined DNA sequences showed thatrninhibition of transcription did not require the localisation of the lesion in the transcribed DNA strand; therefore the damage sensing mechanism has to be different from the direct encounters of transcribing RNA polymerase complexes with DNA damage.rnAltogether, this work provides new evidence that processing of various DNA basernmodifications by BER can perturb transcription of damaged genes by triggering a gene silencing mechanism. As gene expression can be influenced even by a single DNA damage event, this mechanism could have relevance for the endogenous DNA damage induced in cells under normal physiological conditions, with a possible link to gene silencing in general.