Greven H., Van De Kamp T., Dos Santos Rolo T., Baumbach T., Clemen G.

in Vertebrate Zoology, 65 (2015) 81-99.

Abstract

A study on the cranial morphology, especially on the tooth bearing (dental) systems of several preserved developmental stages (from early premetamorphic larvae, in which most skull elements were already present and ossified or ossified in part, to transformed adult) of the smooth newt Lissotriton vulgaris (Salamandridae) was undertaken. We used μCT (to visualize the ossified elements in general and their relationships to each other) and an overall Alizarinred staining (to at best visualize teeth, replacement teeth, tooth buds and, after removing the oral mucosa, the course of dental laminae). Specimens cleared and stained with Alzarinred and Alcianblue were shown to be less suitable for our questions. In one case we used histological sections to follow the course of dental laminae, and in a second case scanning electron microscopy to show the structure of teeth in detail. The general sequence, growth, and changes of the bony elements including the “dental systems”, especially around metamorphosis, known from several other salamandrids are largely confirmed. Concerning the “tooth systems”, metamorphic events include the late appearance of the maxillae, resorption of the coronoids and palatines including their tooth-patches, remodelling of the vomer, i.e. resorption of the vomerine larval tooth-patch, formation of the edentate vomerine plate, and outgrowth of the monstichously dentate vomerine bar (typical for salamandrids). We show evidence that the larval vomer is not completey resorbed and that, unlike what has been described for Salamandra salamandra, the development of the vomerine bar is probably preceded by a shift of the dental lamina towards the middle of the palate, leaving a broad area between larval vomer and dental lamina. We hypothesize that the connective tissue in this area ossifies later and extends posteriorly forming the vomerine bar. It is noteworthy that in nearly all larvae vomer and intact pterygopalatinum were very close together either on one side or on both sides leading in overwintered larvae to the fusion of the vomer and the palatinal portion of the pterygopalatinum, primarily on one side. The zone of fusion is always characterized by a buccal notch. We think that in L. vulgaris the formation of “vomeropterygopalatina” is supported by the close proximity of the two bones and that these bones may fuse due to an imbalance between differentiation- and growth rate (indirectly caused by low temperatures). Approximation and especially fusion of the two bones correspond with the extension of the vomerine dental lamina into the area of the palatine, which temporally provides the latter with teeth. Overwintered larvae show further deviations concerning growth and differentiation of the mouth roof, which can be also interpreted as signs of delayed metamorphosis. They retain, for example, a largely intact dentate palatine, but with some regression of its tooth-patch, while the larval vomer is enlarged anteriorly and posteriorly and its number of teeth has increased; and the largely intact pterygopalatinal bony bridge. Further, maxillae begin to ossify. All larvae obviously have reached a late premetamorphic larval stage before the delay has started.

Brosi M., Caselle M., Hertle E., Hiller N., Kopmann A., Muller A.-S., Schonfeldt P., Schwarz M., Steinmann J.L., Weber M.

in 6th International Particle Accelerator Conference, IPAC 2015 (2015) 882-884.

Abstract

Copyright © 2015 CC-BY-3.0 and by the respective authors. The ANKA storage ring of the Karlsruhe Institute of Technology (KIT) operates in the energy range from 0.5 to 2.5 GeV and generates brilliant coherent synchrotron radiation in the THz range with a dedicated bunch length reducing optic. The producing of radiation in the so-called THz-gap is challenging, but this intense THz radiation is very attractive for certain user experiments. The high degree of compression in this so-called low-alpha optics leads to a complex longitudinal dynamics of the electron bunches. The resulting micro-bunching instability leads to time dependent fluctuations and strong bursts in the radiated THz power. The study of these fluctuations in the emitted THz radiation provides insight into the longitudinal beam dynamics. Fast THz detectors combined with KAPTURE, the dedicated KArlsruhe Pulse Taking and Ultrafast Readout Electronics system developed at KIT, allow the simultaneous measurement of the radiated THz intensity for each bunch individually in a multibunch environment. This contribution gives an overview of the first experience gained using this setup as an online diagnostics tool.

Gehrke R., Kopmann A., Wintersberger E., Beckmann F.

in Synchrotron Radiation News, 28 (2015) 36-42. DOI:10.1080/08940886.2015.1013420

Abstract

© Taylor & Francis. The Helmholtz Association is the largest scientific organization in Germany. It operates all major German research infrastructures involved in research with photons, neutrons, and ions. These are DESY in Hamburg; the Karlsruhe Institute of Technology (KIT); the Research Centre Jülich (FZJ); the Helmholtz Centres in Geesthacht (HZG), Berlin (HZB), and Dresden-Rossendorf (HZDR); and the GSI Centre for research with heavy ions in Darmstadt. In common, all these centers are facing similar challenges related to dramatically increasing data rates and volumes generated with more and more powerful radiation sources together with larger and faster detectors. On the other hand, each center has its own specific portfolio of long-lasting technical expertise in areas like data analysis, information technology, or hardware development. Therefore, it was obvious to address the challenges by acting in concert. This was the main motivation in 2010 for the launch of a joint project among the partners called the “High Data Rate Processing and Analysis Initiative (HDRI).” The initiative is organized into three basic work packages: “Data Management,” “Real-time Data Processing,” and “Data Analysis, Modelling, and Simulation.” The aim is to carry out the development of methods, hardware components, and software for data acquisition, real-time and offline analysis, documentation and archiving, and for remote access to data. The solutions are finally meant to be integrated at the various experimental stations and thus have to be versatile and flexible to cope with the heterogeneous requirements of the different experiments. The claim to create standard solutions makes it mandatory to closely collaborate with large international activities in the field of data handling, like the European PaNdata project (see article in this issue), but also with vendors of detectors, data evaluation software, etc., as well as with corresponding standardization bodies.

Shkarin R., Ametova E., Chilingaryan S., Dritschler T., Kopmann A., Mirone A., Shkarin A., Vogelgesang M., Tsapko S.

in Fundamenta Informaticae, 141 (2015) 245-258. DOI:10.3233/FI-2015-1274

Abstract

© 2015 Fundamenta Informaticae 141.On-line monitoring of synchrotron 3D-imaging experiments requires very fast tomographic reconstruction. Direct Fourier methods (DFM) have the potential to be faster than standard Filtered Backprojection. We have evaluated multiple DFMs using various interpolation techniques. We compared reconstruction quality and studied the parallelization potential. A method using Direct Fourier Inversion (DFI) and a sinc-based interpolation was selected and parallelized for execution on GPUs. Several optimization steps were considered to boost the performance. Finally we evaluated the achieved performance for the latest generation of GPUs from NVIDIA and AMD. The results show that tomographic reconstruction with a throughput of more than 1.5 GB/sec on a single GPU is possible.

Shkarin A., Ametova E., Chilingaryan S., Dritschler T., Kopmann A., Vogelgesang M., Shkarin R., Tsapko S.

in Fundamenta Informaticae, 141 (2015) 259-274. DOI:10.3233/FI-2015-1275

Abstract

© 2015 Fundamenta Informaticae 141. The recent developments in detector technology made possible 4D (3D + time) X-ray microtomographywith high spatial and time resolutions. The resolution and duration of such experiments is currently limited by destructive X-ray radiation. Algebraic reconstruction technique (ART) can incorporate a priori knowledge into a reconstruction model that will allow us to apply some approaches to reduce an imaging dose and keep a good enough reconstruction quality. However, these techniques are very computationally demanding. In this paper we present a framework for ART reconstruction based on OpenCL technology. Our approach treats an algebraic method as a composition of interacting blocks which performdifferent tasks, such as projection selection, minimization, projecting and regularization. These tasks are realised using multiple algorithms differing in performance, the quality of reconstruction, and the area of applicability. Our framework allows to freely combine algorithms to build the reconstruction chain. All algorithms are implemented with OpenCL and are able to run on a wide range of parallel hardware. As well the framework is easily scalable to clustered environment with MPI. We will describe the architecture of ART framework and evaluate the quality and performance on latest generation of GPU hardware from NVIDIA and AMD.