Nanomechanical and phononic properties of structured soft materials

Significant interest in nanotechnology, is stimulated by the fact that materials exhibit qualitative changes of properties when their dimensions approach ”finite-sizes”. Quantization of electronic, optical and acoustic energies at the nanoscale provides novel functions, with interests spanning from electronics and photonics to biology. The present dissertation involves the application of Brillouin light scattering (BLS) to quantify and utilize material displacementsrnfor probing phononics and elastic properties of structured systems with dimensions comparable to the wavelength of visible light. The interplay of wave propagation with materials exhibiting spatial inhomogeneities at sub-micron length scales provides information not only about elastic properties but also about structural organization at those length scales. In addition the vector nature of q allows, for addressing the directional dependence of thermomechanical properties. To meet this goal, one-dimensional confined nanostructures and a biological system possessing high hierarchical organization were investigated. These applications extend the capabilities of BLS from a characterization tool for thin films to a method for unravelingrnintriguing phononic properties in more complex systems.

Parametric editors for structured documents

Lo scopo di questa dissertazione è di identificare le tecnologie più appropriate per la creazione di editor parametrici per documenti strutturati e di descrivere LIME, un editor di markup parametrico e indipendente dal linguaggio. La recente evoluzione delle tecnologie XML ha portato ad un utilizzo sempre più consistente di documenti strutturati. Oggigiorno, questi vengono utilizzati sia per scopi tipografici sia per l’interscambio di dati nella rete internet. Per questa ragione, sempre più persone hanno a che fare con documenti XML nel lavoro quotidiano. Alcuni dialetti XML, tuttavia, non sono semplici da comprendere e da utilizzare e, per questo motivo, si rendono necessari editor XML che possano guidare gli autori di documenti XML durante tutto il processo di markup. In alcuni contesti, specialmente in quello dell’informatica giuridica, sono stati introdotti i markup editor, software WYSIWYG che assistono l’utente nella creazione di documenti corretti. Questi editor possono essere utilizzati anche da persone che non conoscono a fondo XML ma, d’altra parte, sono solitamente basati su uno specifico linguaggio XML. Questo significa che sono necessarie molte risorse, in termini di programmazione, per poterli adattare ad altri linguaggi XML o ad altri contesti. Basando l’architettura degli editor di markup su parametri, è possibile progettare e sviluppare software che non dipendono da uno specifico linguaggio XML e che possono essere personalizzati al fine di utilizzarli in svariati contesti.

Structured antibody surfaces for bio-recognition and a label-free detection of bacteria

Antibody microarrays are of great research interest because of their potential application as biosensors for high-throughput protein and pathogen screening technologies. In this active area, there is still a need for novel structures and assemblies providing insight in binding interactions such as spherical and annulus-shaped protein structures, e.g. for the utilization of curved surfaces for the enhanced protein-protein interactions and detection of antigens. Therefore, the goal of the presented work was to establish a new technique for the label-free detection of bio-molecules and bacteria on topographically structured surfaces, suitable for antibody binding.rnIn the first part of the presented thesis, the fabrication of monolayers of inverse opals with 10 μm diameter and the immobilization of antibodies on their interior surface is described. For this purpose, several established methods for the linking of antibodies to glass, including Schiff bases, EDC/S-NHS chemistry and the biotin-streptavidin affinity system, were tested. The employed methods included immunofluorescence and image analysis by phase contrast microscopy. It could be shown that these methods were not successful in terms of antibody immobilization and adjacent bacteria binding. Hence, a method based on the application of an active-ester-silane was introduced. It showed promising results but also the need for further analysis. Especially the search for alternative antibodies addressing other antigens on the exterior of bacteria will be sought-after in the future.rnAs a consequence of the ability to control antibody-functionalized surfaces, a new technique employing colloidal templating to yield large scale (~cm2) 2D arrays of antibodies against E. coli K12, eGFP and human integrin αvβ3 on a versatile useful glass surface is presented. The antibodies were swept to reside around the templating microspheres during solution drying, and physisorbed on the glass. After removing the microspheres, the formation of annuli-shaped antibody structures was observed. The preserved antibody structure and functionality is shown by binding the specific antigens and secondary antibodies. The improved detection of specific bacteria from a crude solution compared to conventional “flat” antibody surfaces and the setting up of an integrin-binding platform for targeted recognition and surface interactions of eukaryotic cells is demonstrated. The structures were investigated by atomic force, confocal and fluorescence microscopy. Operational parameters like drying time, temperature, humidity and surfactants were optimized to obtain a stable antibody structure.

Temperature dependency of human muscle velocity recovery cycles

Velocity recovery cycles (VRCs) of human muscle action potentials have been proposed as a new technique for studying muscle membrane function. This study was undertaken to determine the temperature dependency of VRC parameters.

Preference for structured environment in zebrafish (Danio rerio) and checker barbs (Puntius oligolepis)

Information about the welfare and husbandry of pet and laboratory fish is scarce although millions of fish are sold in pet shops and used in laboratory research every year. Inadequate housing conditions can cause behavioural problems also in fish since they are complex animals with sophisticated behaviour. In this study, we investigated the influence of environmental complexity on compartment preference and behaviour in zebrafish (Danio rerio) and checker barbs (Puntius oligolepis). For the preference test, large aquaria were divided by two semi-transparent walls of Plexiglas into an empty compartment, a structured compartment enriched with plants and clay pots, and a smaller compartment in-between, where food was provided. For observation, the empty and structured compartments were divided into six zones of similar size by defining three vertical layers and two horizontal areas (back vs. front area). Seven groups of six to nine zebrafish and seven groups of seven or eight checker barbs were observed on four days each (within a time period of ten days) to assess compartment use and activity, and to assess behavioural diversity and use of zones within compartments. Both zebrafish and checker barbs showed a significant preference for the structured compartment. Nevertheless, in neither species did behavioural diversity differ between the empty and structured compartment. Zebrafish used all zones in both compartments to the same extent. Checker barbs, however, used the structured compartment more evenly than the empty compartment, where they mainly used the lower and middle zones. These results suggest that zebrafish and checker barbs have a preference for complex environments. Furthermore, they indicate that the behavioural and ecological needs of fish may vary depending on species, and recommendations for husbandry should be specified at species level. (C) 2011 Elsevier B.V. All rights reserved.

HLA-Bw4 identifies a population of HIV-infected patients with an increased capacity to control viral replication after structured treatment interruption

After structured treatment interruption (STI) of treatment for HIV-1, a fraction of patients maintain suppressed viral loads. Prospective identification of such patients might improve HIV-1 treatment, if selected patients are offered STI.

Three-dimensional surface reconstruction within noncontact diffuse optical tomography using structured light

A main field in biomedical optics research is diffuse optical tomography, where intensity variations of the transmitted light traversing through tissue are detected. Mathematical models and reconstruction algorithms based on finite element methods and Monte Carlo simulations describe the light transport inside the tissue and determine differences in absorption and scattering coefficients. Precise knowledge of the sample's surface shape and orientation is required to provide boundary conditions for these techniques. We propose an integrated method based on structured light three-dimensional (3-D) scanning that provides detailed surface information of the object, which is usable for volume mesh creation and allows the normalization of the intensity dispersion between surface and camera. The experimental setup is complemented by polarization difference imaging to avoid overlaying byproducts caused by inter-reflections and multiple scattering in semitransparent tissue.

From EEG dependency multichannel matching pursuit to sparse topographic EEG decomposition

In this work, we present a multichannel EEG decomposition model based on an adaptive topographic time-frequency approximation technique. It is an extension of the Matching Pursuit algorithm and called dependency multichannel matching pursuit (DMMP). It takes the physiologically explainable and statistically observable topographic dependencies between the channels into account, namely the spatial smoothness of neighboring electrodes that is implied by the electric leadfield. DMMP decomposes a multichannel signal as a weighted sum of atoms from a given dictionary where the single channels are represented from exactly the same subset of a complete dictionary. The decomposition is illustrated on topographical EEG data during different physiological conditions using a complete Gabor dictionary. Further the extension of the single-channel time-frequency distribution to a multichannel time-frequency distribution is given. This can be used for the visualization of the decomposition structure of multichannel EEG. A clustering procedure applied to the topographies, the vectors of the corresponding contribution of an atom to the signal in each channel produced by DMMP, leads to an extremely sparse topographic decomposition of the EEG.