Amstutz C. et al.

in 2016 IEEE-NPSS Real Time Conference, RT 2016 (2016), 7543102. DOI:10.1109/RTC.2016.7543102

Abstract

© 2016 IEEE.A new tracking system is under development for operation in the CMS experiment at the High Luminosity LHC. It includes an outer tracker which will construct stubs, built by correlating clusters in two closely spaced sensor layers for the rejection of hits from low transverse momentum tracks, and transmit them off-detector at 40 MHz. If tracker data is to contribute to keeping the Level-1 trigger rate at around 750 kHz under increased luminosity, a crucial component of the upgrade will be the ability to identify tracks with transverse momentum above 3 GeV/c by building tracks out of stubs. A concept for an FPGA-based track finder using a fully time-multiplexed architecture is presented, where track candidates are identified using a projective binning algorithm based on the Hough Transform. A hardware system based on the MP7 MicroTCA processing card has been assembled, demonstrating a realistic slice of the track finder in order to help gauge the performance and requirements for a full system. This paper outlines the system architecture and algorithms employed, highlighting some of the first results from the hardware demonstrator and discusses the prospects and performance of the completed track finder.

Hahn S., Muller Y., Hofmann R., Moosmann J., Oktem O., Helfen L., Guigay J.-P., Van De Kamp T., Baumbach T.

in Physical Review A – Atomic, Molecular, and Optical Physics, 93 (2016), 053834. DOI:10.1103/PhysRevA.93.053834

Abstract

© 2016 American Physical Society. ©2016 American Physical Society. We analyze theoretically and investigate experimentally the transfer of phase to intensity power spectra of spatial frequencies through free-space Fresnel diffraction. Depending on λz (where λ is the wavelength and z is the free-space propagation distance) and the phase-modulation strength S, we demonstrate that for multiscale and broad phase spectra critical behavior transmutes a quasilinear to a nonlinear diffractogram except for low frequencies. On the contrary, a single-scale and broad phase spectrum induces a critical transition in the diffractogram at low frequencies. In both cases, identifying critical behavior encoded in the intensity power spectra is of fundamental interest because it exhibits the limits of perturbative power counting but also guides resolution and contrast optimization in propagation-based, single-distance, phase-contrast imaging, given certain dose and coherence constraints.

Koenig T., Zuber M., Trimborn B., Farago T., Meyer P., Kunka D., Albrecht F., Kreuer S., Volk T., Fiederle M., Baumbach T.

in Physics in Medicine and Biology, 61 (2016) 3427-3442, 3427. DOI:10.1088/0031-9155/61/9/3427

Abstract

© 2016 Institute of Physics and Engineering in Medicine. The x-ray dark-field contrast accessible via grating interferometry is sensitive to features at length scales well below what is resolvable by a detector system. It is commonly explained as arising from small-angle x-ray scattering (SAXS), and can be implemented both at synchrotron beamlines and with low-brilliance sources such as x-ray tubes. Here, we demonstrate that for tube based setups the underlying process of image formation can be fundamentally different. For focal spots or detector pixels that comprise multiple grating periods, we show that dark-field images contain a strong artificial and system-specific component not arising from SAXS. Based on experiments carried out with a nanofocus x-ray tube and the example of an excised rat lung, we demonstrate that the dark-field contrast observed for porous media transforms into a differential phase contrast for large geometric magnifications. Using a photon counting detector with an adjustable point spread function, we confirm that a dark-field image can indeed be formed by an intra-pixel differential phase contrast that cannot be resolved as such due to a dephasing between the periodicities of the absorption grating and the Talbot carpet. Our findings are further corroborated by a link between the strength of this pseudo-dark-field contrast and our x-ray tube’s focal spot size in a three-grating setup. These results must not be ignored when measurements are intended to be reproducible across systems.

Huang D.-Y., Bechly G., Nel P., Engel M.S., Prokop J., Azar D., Cai C.-Y., Van De Kamp T., Staniczek A.H., Garrouste R., Krogmann L., Dos Santos Rolo T., Baumbach T., Ohlhoff R., Shmakov A.S., Bourgoin T., Nel A.

in Scientific Reports, 6 (2016), 23004. DOI:10.1038/srep23004

Abstract

With nearly 100,000 species, the Acercaria (lice, plant lices, thrips, bugs) including number of economically important species is one of the most successful insect lineages. However, its phylogeny and evolution of mouthparts among other issues remain debatable. Here new methods of preparation permitted the comprehensive anatomical description of insect inclusions from mid-Cretaceous Burmese amber in astonishing detail. These “missing links” fossils, attributed to a new order Permopsocida, provide crucial evidence for reconstructing the phylogenetic relationships in the Acercaria, supporting its monophyly, and questioning the position of Psocodea as sister group of holometabolans in the most recent phylogenomic study. Permopsocida resolves as sister group of Thripida + Hemiptera and represents an evolutionary link documenting the transition from chewing to piercing mouthparts in relation to suction feeding. Identification of gut contents as angiosperm pollen documents an ecological role of Permopsocida as early pollen feeders with relatively unspecialized mouthparts. This group existed for 185 million years, but has never been diverse and was superseded by new pollenivorous pollinators during the Cretaceous co-evolution of insects and flowers. The key innovation of suction feeding with piercing mouthparts is identified as main event that triggered the huge post-Carboniferous radiation of hemipterans, and facilitated the spreading of pathogenic vectors.

Rota L., Vogelgesang M., Perez L.E.A., Caselle M., Chilingaryan S., Dritschler T., Zilio N., Kopmann A., Balzer M., Weber M.

in Journal of Instrumentation, 11 (2016), P02007. DOI:10.1088/1748-0221/11/02/P02007

Abstract

© 2016 IOP Publishing Ltd and Sissa Medialab srl.Modern physics experiments produce multi-GB/s data rates. Fast data links and high performance computing stages are required for continuous data acquisition and processing. Because of their intrinsic parallelism and computational power, GPUs emerged as an ideal solution to process this data in high performance computing applications. In this paper we present a high-throughput platform based on direct FPGA-GPU communication. The architecture consists of a Direct Memory Access (DMA) engine compatible with the Xilinx PCI-Express core, a Linux driver for register access, and high- level software to manage direct memory transfers using AMD’s DirectGMA technology. Measurements with a Gen3 x8 link show a throughput of 6.4 GB/s for transfers to GPU memory and 6.6 GB/s to system memory. We also assess the possibility of using the architecture in low latency systems: preliminary measurements show a round-trip latency as low as 1 μs for data transfers to system memory, while the additional latency introduced by OpenCL scheduling is the current limitation for GPU based systems. Our implementation is suitable for real-time DAQ system applications ranging from photon science and medical imaging to High Energy Physics (HEP) systems.

Schwermann A.H., dos Santos Rolo T., Caterino M.S., Bechly G., Schmied H., Baumbach T., van de Kamp T.

in eLife, 5 (2016), e12129. DOI:10.7554/eLife.12129

Abstract

© Schwermann et al. External and internal morphological characters of extant and fossil organisms are crucial to establishing their systematic position, ecological role and evolutionary trends. The lack of internal characters and soft-tissue preservation in many arthropod fossils, however, impedes comprehensive phylogenetic analyses and species descriptions according to taxonomic standards for Recent organisms. We found well-preserved three-dimensional anatomy in mineralized arthropods from Paleogene fissure fillings and demonstrate the value of these fossils by utilizing digitally reconstructed anatomical structure of a hister beetle. The new anatomical data facilitate a refinement of the species diagnosis and allowed us to reject a previous hypothesis of close phylogenetic relationship to an extant congeneric species. Our findings suggest that mineralized fossils, even those of macroscopically poor preservation, constitute a rich but yet largely unexploited source of anatomical data for fossil arthropods.

Caselle M., Blank T., Colombo F., Dierlamm A., Husemann U., Kudella S., Weber M.

in Journal of Instrumentation, 11 (2016), C01050. DOI:10.1088/1748-0221/11/01/C01050

Abstract

© 2016 IOP Publishing Ltd and Sissa Medialab srl.In the next generation of collider experiments detectors will be challenged by unprecedented particle fluxes. Thus large detector arrays of highly pixelated detectors with minimal dead area will be required at reasonable costs. Bump-bonding of pixel detectors has been shown to be a major cost-driver. KIT is one of five production centers of the CMS barrel pixel detector for the Phase I Upgrade. In this contribution the SnPb bump-bonding process and the production yield is reported. In parallel to the production of the new CMS pixel detector, several alternatives to the expensive photolithography electroplating/electroless metal deposition technologies are developing. Recent progress and challenges faced in the development of bump-bonding technology based on gold-stud bonding by thin (15 μm) gold wire is presented. This technique allows producing metal bumps with diameters down to 30 μm without using photolithography processes, which are typically required to provide suitable under bump metallization. The short setup time for the bumping process makes gold-stud bump-bonding highly attractive (and affordable) for the flip-chipping of single prototype ICs, which is the main limitation of the current photolithography processes.

Briceno R.D., Eberhard W.G., Chinea-Cano E., Wegrzynek D., Dos Santos Rolo T.

in Ethology Ecology and Evolution, 28 (2016) 53-76. DOI:10.1080/03949370.2014.1002114

Abstract

© 2015 Dipartimento di Biologia, Università di Firenze, Italia. A long-standing question in morphological evolution is why male genitalia tend to diverge more rapidly than other structures. One possible explanation is that male genitalia are under sexual selection to function as internal courtship devices. Males of closely related species may provide divergent stimulation using different genital morphologies and behaviors. Testing this hypothesis has been difficult, however, because the presumed genital courtship behavior is often hidden from view inside the female, and because studies of how the males genitalia interact with those of the female are nearly always limited to a single species in a given group, thus restricting opportunities for comparison of closely related species. We present new morphological and behavioral data for portions of the male genitalia that are hidden in the female during copulation in five species in the tsetse fly genus Glossina using data from dissections of pairs frozen in copula, artificially stimulated males, and from copulating pairs viewed with a new X-ray technique that allows events inside the female to be recorded in real time. These data almost certainly give only an incomplete view of this complex, previously hidden world. But even so they clearly reveal that, as predicted by sexual selection theory, the male genitalia of Glossina flies perform dramatic, stereotyped, rhythmic movements deep within the females reproductive tract and in inward folds of her external surface, and that many of these movements probably differ among closely related species. Most of the movements are not explicable as means by which the male anchors himself more securely to the female; all are likely to result in stimulation of the female. A female Glossina can be stimulated tactilely at a given moment during copulation at up to 8-10 or more different sites on her body.

van de Kamp T., Riedel A., Greven H.

in Arthropod Structure and Development, 45 (2016) 14-22. DOI:10.1016/j.asd.2015.10.002

Abstract

© 2015 Elsevier Ltd.The elytral cuticle of 40 beetle species, comprising 14 weevils (Curculionoidea) and 26 representatives of other taxa, is examined. All weevils and 18 other species have an endocuticle with prominent macrofibers, which corresponds to a modified pseudo-orthogonal cuticle. Angles between successive layers of macrofibers range between 30° and 90°, but are constantly less than 60° in weevils. In all Curculionoidea, as well as in one buprestid and one erotylid species exo- and endocuticle are densely interlocked. In the weevil Sitophilus granarius, transmission electron microscopy revealed vertical microfibrils extending from the exocuticle between the macrofibers of the underlaying endocuticle. Vertical microfibrils connecting successive macrofiber layers of the endocuticle were observed in S. granarius and Trigonopterus nasutus. Distinct cuticular characters are traced on a beetle phylogeny: the angles between unidirectional endocuticle layers; the presence and the shape of endocuticular macrofibers; and the interlocking of exo- and endocuticle. While character traits seem to be more or less randomly distributed among Coleoptera, the Curculionoidea have a uniform groundplan: The “weevil-specific” combination of characters includes 1) interlocking of exo- and endocuticle, 2) an endocuticle with distinct ovoid macrofibers embedded in a matrix and 3) comparatively small angles between successive endocuticular layers. Thus, phylogenetic constraints appear equally important to functional factors in the construction of the weevil elytron.

Bruckner A., Wehner K., Neis M., Heethoff M.

in Acarologia, 56 (2016).

Abstract

© Brückner A. et al. Oribatid mites represent a diverse group of soil micro-arthropods. They have evolved a broad range of defensive chemical and morphological traits (e.g. sclerotization, ptychoidy, biomineralization). Chemical defense, rather than sclerotization, can provide protection against large predators (staphylinid beetles) and many oribatid mite species are also well protected against gamasid soil mites using morphological traits (“enemy-free-space hypothesis”). However, since predatory mites and staphylinid beetles have different types of attacking and feeding, the adaptive values of chemical and morphological traits might differ accordingly. We used the oribatid model species Archegozetes longisetosus Aoki and the common gamasid mite Stratiolaelaps miles Berlese in a predator-prey experiment. We tested for effects of chemical defense (treatments with and without oil gland secretions) and sclerotization (treatments with unsclerotized tritonymphs and sclerotized adults) in an orthogonal design. In contrast to attacks by large predators, chemical defense was mostly ineffective against gamasid mites. Sclerotization, however, had a positive effect. Hence, in a natural environment with diverse types of predators, the “enemy-free space” seems only realizable by combinations of chemical and morphological protective traits.