ChlamyCyc - a comprehensive database and web-portal centered on _Chlamydomonas reinhardtii_

*Background* - The unicellular green alga _Chlamydomonas reinhardtii_ is an important eukaryotic model organism for the study of photosynthesis and growth, as well as flagella development and other cellular processes. In the era of high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the whole cellular system of a single organism.
*Results* - In the framework of the German Systems Biology initiative GoFORSYS a pathway/genome database and web-portal for _Chlamydomonas reinhardtii_ (ChlamyCyc) was established, which currently features about 270 metabolic pathways with related genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification.
*Conclusion* - Chlamycyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in _Chlamydomonas reinhardtii_. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de

Classification of braids which give rise to interchange

It is well known that the existence of a braiding in a monoidal category V allows many structures to be built upon that foundation. These include a monoidal 2-category V-Cat of enriched categories and functors over V, a monoidal bicategory V-Mod of enriched categories and modules, a category of operads in V and a 2-fold monoidal category structure on V. We will begin by focusing our exposition on the first and last in this list due to their ability to shed light on a new question. We ask, given a braiding on V, what non-equal structures of a given kind in the list exist which are based upon the braiding. For instance, what non-equal monoidal structures are available on V-Cat, or what non-equal operad structures are available which base their associative structure on the braiding in V. We demonstrate alternative underlying braids that result in an infinite family of associative structures. The external and internal associativity diagrams in the axioms of a 2-fold monoidal category will provide us with several obstructions that can prevent a braid from underlying an associative structure.Comment: Previous title: Equivalence of associative structures over a braiding. This journal ready version adds proof details involving the free braided category with dual

The EU's Eastern Partnership - a misunderstood offer of cooperation

"The European Union's Eastern Partnership, initiated by Poland and Sweden, may fall through without ever having really gotten off the ground. Sweden, the current holder of the EU's rotating presidency, has failed to give the deserved priority and attention to its own initiative. In Russia, the fear is that the EU is seeking to strengthen its influence in the East. Meanwhile, the leadership of Ukraine, one of the strategically most important target countries of the Partnership, opposes the initiative. As such, EU members, the target countries, and Russia misunderstand the purpose of the proposed partnership. It is important to use the Eastern Partnership as a basis for developing a essentially new policy towards EU's neighbors in the East. The Eastern Partnership is of fundamental importance for European energy supplies and the future viability of the EU. Therefore, the EU countries finally must commit themselves to a strategic development of this region and conduct an interests-oriented neighborhood policy that integrates or, if necessary, pressures Russia." (author's abstract) "Die polnisch-schwedische Initiative einer Östlichen Partnerschaft der EU könnte scheitern, bevor sie überhaupt richtig begonnen hat. Denn die schwedische EU-Ratspräsidentschaft behandelt ihre eigene Initiative nicht prioritär und verleiht der Östlichen Partnerschaft so nicht das Gewicht, das sie bräuchte. In Russland besteht der Verdacht, die EU wolle ihr Einflussgebiet weiter in den Osten verlagern. Und in den Adressatenstaaten opponiert gerade in der strategisch wichtigen Ukraine die Führung gegen die neue EU-Initiative. Dabei fehlinterpretieren einige EU-Staaten, die Adressaten-Länder und Russland die Rolle dieser Initiative. Wichtig wäre, die Östliche Partnerschaft als Grundlage für eine substanziell neue Politik gegenüber den östlichen Nachbarstaaten der EU zu entwickeln. Die östliche Nachbarschaft ist von entscheidender Bedeutung für die europäische Energieversorgung und für die Zukunftsfähigkeit der Union. Deswegen müssen sich die EU-Staaten endlich zur strategischen Entwicklung dieser Region bekennen und eine interessenorientierte Nachbarschaftspolitik unter Einbeziehung von, aber – falls nötig – auch mit Druck auf Russland betreiben." [Autorenreferat

Artificial Intelligence for Lameness Detection in Horses-A Preliminary Study

Simple Summary In the expanding field of artificial intelligence, deep learning and smart-device-technology, a diagnostic software tool was developed, which can help distinguish between lame and sound horses and locate the affected limb. As lameness influences the welfare of horses and is often difficult to detect, this tool can help owners and veterinarians in the process of evaluation. The technology is based on pose estimation, which is already used in human and veterinary science to study movement of limbs or bodies without the need to fix any devices onto the object of interest. In this study, 22 horses with unilateral fore- or hindlimb lameness and a control group of eight sound horses were analysed with the program. Based on the results of the program, it was possible to differentiate between horses with fore- and hindlimb lameness and sound horses. Difficult light settings, such as direct sunlight or darkness, or very even-coloured coats, complicate the precise placement of reference points. The analysis and detection with software-generated movement trajectories using pose estimation is very promising but requires further development. Lameness in horses is a long-known issue influencing the welfare, as well as the use, of a horse. Nevertheless, the detection and classification of lameness mainly occurs on a subjective basis by the owner and the veterinarian. The aim of this study was the development of a lameness detection system based on pose estimation, which permits non-invasive and easily applicable gait analysis. The use of 58 reference points on easily detectable anatomical landmarks offers various possibilities for gait evaluation using a simple setup. For this study, three groups of horses were used: one training group, one analysis group of fore and hindlimb lame horses and a control group of sound horses. The first group was used to train the network;afterwards, horses with and without lameness were evaluated. The results show that forelimb lameness can be detected by visualising the trajectories of the reference points on the head and both forelimbs. In hindlimb lameness, the stifle showed promising results as a reference point, whereas the tuber coxae were deemed unsuitable as a reference point. The study presents a feasible application of pose estimation for lameness detection, but further development using a larger dataset is essential

GPU-Accelerated nearest neighbor search for 3d registration

Abstract. Nearest Neighbor Search (NNS) is employed by many computer vision algorithms. The computational complexity is large and constitutes a challenge for real-time capability. The basic problem is in rapidly processing a huge amount of data, which is often addressed by means of highly sophisticated search methods and parallelism. We show that NNS based vision algorithms like the Iterative Closest Points algorithm (ICP) can achieve real-time capability while preserving compact size and moderate energy consumption as it is needed in robotics and many other domains. The approach exploits the concept of general purpose computation on graphics processing units (GPGPU) and is compared to parallel processing on CPU. We apply this approach to the 3D scan registration problem, for which a speed-up factor of 88 compared to a sequential CPU implementation is reported

3D Cameras: 3D Computer Vision of Wide Scope

The human visual sense is the one among all other senses that gathers most information we receive. Evolution has optimized our visual system to negotiate one's way in three dimensions even through cluttered environments. For perceiving 3D information, the human brain uses three important principles: stereo vision, motion parallax and a-priori knowledge about the perspective appearance of objects in dependency of their distance. These tasks pose a challenge to computer vision since decades. Today the most common techniques for 3D sensing are CCD- or CMOS-camera, laser scanner or 3D time-of-flight camera based. Even though evolution has shown predominance for passive stereo vision systems, three additional problems are remaining for 3D perception compared with the two mentioned active vision systems above. First, the computation needs a great deal of performance, since the correlation of two images from a different point of view has to be found. Second, distances to structureless surfaces cannot be measured, if the perspective projection of the object is larger than the camera’s field of view. This problem is often called aperture problem. Finally, a passive visual sensor has to cope with shadowing effects and changes in illumination over time. That is why for mapping purposes mostly active vision systems like laser scanners are used , e.g. [Thrun et al., 2000], [Wulf & Wagner, 2003], [Surmann et al., 2003]. But these approaches are usually not applicable to tasks considering environment dynamics. Due to this restriction, 3D cameras [CSEM SA, 2007], [PMDTec, 2007] have attracted attention since their invention nearly a decade ago. Distance measurements are also based on a time-of-flight principle but with an important difference. Instead of sampling laser beams serially to acquire distance data point-wise, the entire scene is measured in parallel with a modulated surface. This principle allows for higher frame rates and thus enables the consideration of environment dynamics. The first part of this chapter discusses the physical principles of 3D sensors, which are commonly used in the robotics community for typical problems like mapping and navigation. The second part concentrates on 3D cameras, their assets, drawbacks and perspectives. Based on these examining parts, some solutions are discussed that handle common problems occurring in dynamic environments with changing lighting conditions. Finally, it is shown in the last part of this chapter how 3D cameras can be applied to mapping, object localization and feature tracking tasks

Splines for damage and fracture in solids

This thesis addresses different aspects of numerical fracture mechanics and spline technology for analysis. An energy-based arc-length control for physically non-linear problems is proposed. It switches between an internal energy-based and a dissipation-based arc-length method. The arc-length control allows to trace an equilibrium path with multiple snap-through and/or snap-back phenomena and only requires two parameters. Phase field models for brittle and cohesive fracture are numerically assessed. The impact of different parameters and boundary conditions on the phase field model for brittle fracture is investigated. It is demonstrated that Γ-convergence is not attained numerically for the phase field model for brittle fracture and that the phase field model for cohesive fracture does not pass a two-dimensional patch test when using an unstructured mesh. The properties of the Bézier extraction operator for T-splines are exploited for the determination of linear dependencies, partition of unity properties, nesting behaviour and local refinement. Unstructured T-spline meshes with extraordinary points are modified such that the blending functions fulfil the partition of unity property and possess a higher continuity. Bézier extraction for Powell-Sabin B-splines is introduced. Different spline technologies are compared when solving Kirchhoff-Love plate theory on a disc with simply supported and clamped boundary conditions. Powell-Sabin B-splines are utilised for smeared and discrete approaches to fracture. Due to the higher continuity of Powell-Sabin B-splines, the implicit fourth order gradient damage model for quasi-brittle materials can be solved and stresses can be computed directly at the crack tip when considering the cohesive zone method