Punctured Trellis-Coded Modulation

In classic trellis-coded modulation (TCM) signal constellations of twice the cardinality are applied when compared to an uncoded transmission enabling transmission of one bit of redundancy per PAM-symbol, i.e., rates of $\frac{K}{K+1}$ when $2^{K+1}$ denotes the cardinality of the signal constellation. In order to support different rates, multi-dimensional (i.e., $\mathcal{D}$-dimensional) constellations had been proposed by means of combining subsequent one- or two-dimensional modulation steps, resulting in TCM-schemes with $\frac{1}{\mathcal{D}}$ bit redundancy per real dimension. In contrast, in this paper we propose to perform rate adjustment for TCM by means of puncturing the convolutional code (CC) on which a TCM-scheme is based on. It is shown, that due to the nontrivial mapping of the output symbols of the CC to signal points in the case of puncturing, a modification of the corresponding Viterbi-decoder algorithm and an optimization of the CC and the puncturing scheme are necessary.Comment: 5 pages, 10 figures, submitted to IEEE International Symposium on Information Theory 2013 (ISIT

Structure determination of membrane proteins by electron crystallography

A fundamental principle of life is the separation of environments into different compartments. Prokaryotes shield their interior from the environment by a plasma membrane and in some cases also by a cell wall. Eukaryotes refine this compartmentalization by building different organelles for different parts of the cell metabolism. Nevertheless, these different compartments are dependent on each other and are interconnected by membrane proteins that transport specific nutrients, hormones, ions, water and waste products across the membrane and facilitate signal transmission between different compartments. Understanding the structure and function of membrane proteins can therefore allow an enormous insight into the regulation of different metabolic pathways. The electron microscope (EM) proved itself a great tool for studying membrane proteins, offering the unique opportunity to image membrane proteins within a lipid bilayer as close to the natural conditions as possible. Processing of images acquired by an electron microscope poses a challenging task for both scientist and processing hardware. Newly developed and optimized algorithms are needed to improve the image processing to a level that allows atomic resolution to be achieved regularly. Membrane proteins pose a difficult challenge for a structural biologist. To crystallize membrane proteins into well ordered two dimensional (2D) or three dimensional (3D) crystals is one of the most important prerequisites for structural analysis at the atomic level, yet membrane proteins are notoriously difficult to crystallize. One exception may be bacteriorhodopsin, which forms near-perfect crystals already in its native membrane. This may explain the fact that the first 2D electron crystallographic structure determined at 7 Å resolution by Henderson and Unwin[20][43] in 1975 was the structure of bacteriorhodopsin. In 1990 the structure of Br was determined to atomic resolution by Henderson et al.[19], being the first atomic structure of a membrane protein. The structure determination of Br was also the starting point for the mrc program suite, which is widely used at the moment in the, albeit small, 2D electron crystallography community. Using the mrc software Kühlbrandt et al.[26] solved the structure of the light-harvesting chlorophyll a/b-protein complex in 1994. For recording the images they used the spot scan technique developed by Downing in 1991[9]. The first aquaporin water channel determined was aquaporin 1, resolved by Walz et al. in 1997[45] at 6 Å resolution, and subsequently solved to atomic resolution by Murata et al. in 2000[29]. Recently, several more aquaporin structures were determined by 2D electron crystallographic methods, aquaporin-0 (AQP0) by Gonen et al. in 2004[14] at 3 Å and in 2005[13] at 1.9 Å and aquaporin-4 (AQP4) by Hiroaki et al. in 2006[22]. Interestingly, AQP4 shows exactly the same monomer arrangement as SoPIP2;1. The recent publications show that the trend goes from recording solely images to the recording of diffraction data in combination with images or even to recording diffraction data exclusively, and then using methods developed for x-ray crystallography to obtain the phase information. Given the fact that the software available for processing of 2D electron diffraction patterns is less evolved than the one for processing images, and given this new development of increased usage of diffraction patterns, it only makes sense to focus on implementing new and improved programs for 2D electron diffraction processing. In this work I would like to present the advances I achieved in the structural determination of aquaporin 2, as well as my contribution to other projects, in particular the structural investigations of SoPIP2;1 and KdgM. I will also explain the modified sample preparation methods which made data recording at high tilt angles more reliable and achieved an improvement in resolution of the measured data. A second, equally important and detailed part of my thesis is the work invested in improving and extending the image processing to a point where a user, not adept in programming in several languages, can use it and produce good results. For this I improved the functionality and performance at several points, including a strong emphasis on user friendliness and ease of maintenance

Validity of pressure pain thresholds in female workers with and without recurrent low back pain

Recurrent low back pain (LBP) is a common pain condition in elderly workers in a variety of occupations, but little is known about its origin and the mechanisms leading to an often disabling sensation of pain that may be persistent or intermittent. In the present study we evaluated the pressure pain thresholds (PPTs) in subjects suffering from recurrent LBP, as well as in healthy controls, to investigate if recurrent LBP is associated with an increased sensitivity of the muscular and ligamentous structures located on the lower back. One hundred and six female workers, aged between 45 and 62years and working either in administrative or nursing professions were examined. The subjects were classified into LBP cases and controls based on the Nordic questionnaire. Subjects indicating 8-30 or more days with LBP during the past 12months were graded as cases. PPTs were measured on 12 points (six on each side of the body) expected to be relevant for LBP (paravertebral muscles, musculus quadratus lumborum, os ilium, iliolumbar ligament, musculus piriformis and greater trochanter), as well as on a reference point (middle of the forehead) using a digital dolorimeter. The PPTs on all points on the lower back highly correlated with each other and a high internal consistency was found with a Cronbach alpha coefficient >0.95. There was a moderate and significant correlation of the PPT on the forehead with the PPT on the lower back with correlation coefficients ranging from 0.36 to 0.49. In LBP cases from administrative professions, the PPT on the forehead was significantly decreased (P<0.05). The PPT on the lower back did not significantly differ between the four groups studied, namely nurses and administrative workers with and without recurrent LBP. These results give evidence that recurrent LBP is not associated with an altered sensitivity of the muscular and myofascial tissues in the lumbar region. Furthermore, they raise questions about the value of reference point measurements in recurrent LB

Matching-based preprocessing algorithms to the solution of saddle-point problems in large-scale nonconvex interior-point optimization

Interior-point methods are among the most efficient approaches for solving large-scale nonlinear programming problems. At the core of these methods, highly ill-conditioned symmetric saddle-point problems have to be solved. We present combinatorial methods to preprocess these matrices in order to establish more favorable numerical properties for the subsequent factorization. Our approach is based on symmetric weighted matchings and is used in a sparse direct LDL T factorization method where the pivoting is restricted to static supernode data structures. In addition, we will dynamically expand the supernode data structure in cases where additional fill-in helps to select better numerical pivot elements. This technique can be seen as an alternative to the more traditional threshold pivoting techniques. We demonstrate the competitiveness of this approach within an interior-point method on a large set of test problems from the CUTE and COPS sets, as well as large optimal control problems based on partial differential equations. The largest nonlinear optimization problem solved has more than 12 million variables and 6 million constraint