Showing papers by "Fraunhofer Society published in 2009"

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

Abstract: With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most of the underlying matching models neglect the necessity to allow not only mismatches, but also insertions and deletions. Current evaluations indicate, however, that very different error models apply to the novel high-throughput sequencing methods. While the most frequent error-type in Illumina reads are mismatches, reads produced by 454's GS FLX predominantly contain insertions and deletions (indels). Even though 454 sequencers are able to produce longer reads, the method is frequently applied to small RNA (miRNA and siRNA) sequencing. Fast and accurate matching in particular of short reads with diverse errors is therefore a pressing practical problem. We introduce a matching model for short reads that can, besides mismatches, also cope with indels. It addresses different error models. For example, it can handle the problem of leading and trailing contaminations caused by primers and poly-A tails in transcriptomics or the length-dependent increase of error rates. In these contexts, it thus simplifies the tedious and error-prone trimming step. For efficient searches, our method utilizes index structures in the form of enhanced suffix arrays. In a comparison with current methods for short read mapping, the presented approach shows significantly increased performance not only for 454 reads, but also for Illumina reads. Our approach is implemented in the software segemehl available at http://www.bioinf.uni-leipzig.de/Software/segemehl/.

Sequence control in polymer synthesis

Abstract: The control over comonomer sequences is barely studied in macromolecular science nowadays. This is an astonishing situation, taking into account that sequence-defined polymers such as nucleic acids and proteins are key components of the living world. In fact, fascinating biological machines such as enzymes, transport proteins, cytochromes or sensory receptors would certainly not exist if evolution had not favored chemical pathways for controlling chirality and sequences. Thus, it seems obvious that synthetic polymers with controlled monomer sequences have an enormous role to play in the materials science of the next centuries. The goal of this tutorial review is to shed light on this highly important but embryonic field of research. Both biological and synthetic mechanisms for controlling sequences in polymerization processes are critically discussed herein. This state-of-the-art overview may serve as a source of inspiration for the development of new generations of synthetic macromolecules.

Greatly Increased Toughness of Infiltrated Spider Silk

Abstract: In nature, tiny amounts of inorganic impurities, such as metals, are incorporated in the protein structures of some biomaterials and lead to unusual mechanical properties of those materials. A desire to produce these biomimicking new materials has stimulated materials scientists, and diverse approaches have been attempted. In contrast, research to improve the mechanical properties of biomaterials themselves by direct metal incorporation into inner protein structures has rarely been tried because of the difficulty of developing a method that can infiltrate metals into biomaterials, resulting in a metal-incorporated protein matrix. We demonstrated that metals can be intentionally infiltrated into inner protein structures of biomaterials through multiple pulsed vapor-phase infiltration performed with equipment conventionally used for atomic layer deposition (ALD). We infiltrated zinc (Zn), titanium (Ti), or aluminum (Al), combined with water from corresponding ALD precursors, into spider dragline silks and observed greatly improved toughness of the resulting silks. The presence of the infiltrated metals such as Al or Ti was verified by energy-dispersive x-ray (EDX) and nuclear magnetic resonance spectra measured inside the treated silks. This result of enhanced toughness of spider silk could potentially serve as a model for a more general approach to enhance the strength and toughness of other biomaterials.

The effects of multiview depth video compression on multiview rendering

Abstract: This article investigates the interaction between different techniques for depth compression and view synthesis rendering with multiview video plus scene depth data Two different approaches for depth coding are compared, namely H264/MVC, using temporal and inter-view reference images for efficient prediction, and the novel platelet-based coding algorithm, characterized by being adapted to the special characteristics of depth-images Since depth-images are a 2D representation of the 3D scene geometry, depth-image errors lead to geometry distortions Therefore, the influence of geometry distortions resulting from coding artifacts is evaluated for both coding approaches in two different ways First, the variation of 3D surface meshes is analyzed using the Hausdorff distance and second, the distortion is evaluated for 2D view synthesis rendering, where color and depth information are used together to render virtual intermediate camera views of the scene The results show that-although its rate-distortion (R-D) performance is worse-platelet-based depth coding outperforms H264, due to improved sharp edge preservation Therefore, depth coding needs to be evaluated with respect to geometry distortions

CD4-Positive T Lymphocytes Provide a Neuroimmunological Link in the Control of Adult Hippocampal Neurogenesis

Abstract: Adult hippocampal neurogenesis occurs in an exceptional permissive microenvironment. Neuroimmunological mechanisms might be prominently involved in the endogenous homeostatic principles that control baseline levels of adult neurogenesis. We show in this study that this homeostasis is partially dependent on CD4-positive T lymphocytes. Systemic depletion of CD4-positive T lymphocytes led to significantly reduced hippocampal neurogenesis, impaired reversal learning in the Morris water maze, and decreased brain-derived neurotrophic factor expression in the brain. No such effect of CD8 or B cells was observed. Repopulation of RAG2(-/-) mice with CD4, but not with CD8 cells again increased precursor cell proliferation. The T cells in our experiments were non-CNS specific and rarely detectable in the healthy brain. Thus, we can exclude cell-cell contacts between immune and brain cells or lymphocyte infiltration into the CNS as a prerequisite for an effect of CD4-T cells on neurogenesis. We propose that systemic CD4-T cell activity is required for maintaining cellular plasticity in the adult hippocampus and represents an evolutionary relevant communication route for the brain to respond to environmental changes.

Advanced spinel and sub-μm Al2O3 for transparent armour applications

Abstract: Hardness is important for a high ballistic strength, and with HV10 = 20–22 GPa sintered sub-μm Al 2 O 3 is the hardest of all transparent materials for compact windows. However, light transmission through polycrystalline Al 2 O 3 is limited by birefringent scattering losses: high transmissions are known at larger IR wavelengths for grain sizes of about 0.5 μm but the visible real in-line transmission RIT is only 70–75% of the theoretical maximum at 0.8–1 mm thickness. These losses will be the higher for thicker components whereas a safe ballistic performance requires 1.5–2 mm thickness at least. New technologies bring the transmission closer to the limit associating grain sizes of 0.3 μm with an RIT of 84–93% of the theoretical maximum (thickness 0.8 mm). However, even these extreme results give again rise to doubt that it will ever be possible to manufacture larger and thicker Al 2 O 3 windows with a sufficiently high transparency. On the other hand, new results are presented for fine-grained spinel with RIT close to the theoretical maximum and with a hardness that approaches sapphire. In first ballistic tests this spinel outperformed sapphire of different orientations. It is, therefore, suggested that sub-μm Al 2 O 3 may be a good choice for IR windows or as armour for low threat applications where thinner tiles can be used. Most threats, however, require thicker windows where the new spinel appears as one of the most favourable candidates.

Argon plasma sintering of inkjet printed silver tracks on polymer substrates

Abstract: An alternative and selective sintering method for the fabrication of conductive silver tracks on common polymer substrates is presented, by exposure to low-pressure argon plasma. Inkjet printing has been used to pattern a silver nanoparticle ink. This resulted in conductive features with a resistivity less than one order of magnitude higher than the bulk value of silver without affecting the polymer substrate. This process may be employed in the production of conductive features with low material usage on common polymer substrates in, for example, printed electronics.

Interactive visual clustering of large collections of trajectories

Abstract: One of the most common operations in exploration and analysis of various kinds of data is clustering, i.e. discovery and interpretation of groups of objects having similar properties and/or behaviors. In clustering, objects are often treated as points in multi-dimensional space of properties. However, structurally complex objects, such as trajectories of moving entities and other kinds of spatio-temporal data, cannot be adequately represented in this manner. Such data require sophisticated and computationally intensive clustering algorithms, which are very hard to scale effectively to large datasets not fitting in the computer main memory. We propose an approach to extracting meaningful clusters from large databases by combining clustering and classification, which are driven by a human analyst through an interactive visual interface.

Robotic home assistant Care-O-bot ® 3 - product vision and innovation platform

Abstract: The development of a mobile robot to assist people in their home is a long term goal of Fraunhofer IPA. As a vision of a future household product, the latest prototype, Care-O-bot® 3, is equipped with the latest industrial state-of-the art hardware components and offers all modern multimedia and interaction equipment as well as most advanced sensors and control. Care-O-bot® 3 has been presented to the public on several occasions where it distributed drinks to the visitors of trade fairs and events. Current developments aim at applying the robot in an eldercare facility in order to support the personnel in their daily tasks.

An experimental comparison of chemical traits and litter decomposition rates in a diverse range of subarctic bryophyte, lichen and vascular plant species

Abstract: 1. Climate change in the subarctic is expected to influence vegetation composition, specifically bryophyte and lichen communities, thereby modifying litter decomposition rates and carbon (C) dynami ...

PDB_REDO : automated re-refinement of X-ray structure models in the PDB

Abstract: Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

CADx of mammographic masses and clustered microcalcifications: a review.

Abstract: Breast cancer is the most common type of cancer among women in the western world. While mammography is regarded as the most effective tool for the detection and diagnosis of breast cancer, the interpretation of mammograms is a difficult and error-prone task. Hence, computer aids have been developed that assist the radiologist in the interpretation of mammograms. Computer-aided detection (CADe) systems address the problem that radiologists often miss signs of cancers that are retrospectively visible in mammograms. Furthermore, computer-aided diagnosis (CADx) systems have been proposed that assist the radiologist in the classification of mammographic lesions as benign or malignant. While a broad variety of approaches to both CADe and CADx systems have been published in the past two decades, an extensive survey of the state of the art is only available for CADe approaches. Therefore, a comprehensive review of the state of the art of CADx approaches is presented in this work. Besides providing a summary, the goals for this article are to identify relations, contradictions, and gaps in literature, and to suggest directions for future research. Because of the vast amount of publications on the topic, this survey is restricted to the two most important types of mammographic lesions: masses and clustered microcalcifications. Furthermore, it focuses on articles published in international journals.

400W Yb:YAG Innoslab fs-Amplifier.

Abstract: The Innoslab design, already established for neodymium doped laser crystals, was applied to ytterbium doped laser materials. Recent progresses in brightness of high power diode lasers facilitate efficient pumping of quasi-three-level laser materials. Innoslab amplifiers are compared to competing thin-disk and fiber fs-amplifiers. A compact diode-pumped Yb:YAG Innoslab fs-oscillator-amplifier system, scalable to the kilowatt range, was realized. Numerical simulations result in conditions for high efficiency and beam quality. Nearly transform and diffraction limited 680 fs pulses at 400 W average output power and 76 MHz repetition rate without using CPA technology have been achieved at room temperature so far.

Integrated wireless neural interface based on the Utah electrode array.

Abstract: This report presents results from research towards a fully integrated, wireless neural interface consisting of a 100-channel microelectrode array, a custom-designed signal processing and telemetry IC, an inductive power receiving coil, and SMD capacitors. An integration concept for such a device was developed, and the materials and methods used to implement this concept were investigated. We developed a multi-level hybrid assembly process that used the Utah Electrode Array (UEA) as a circuit board. The signal processing IC was flip-chip bonded to the UEA using Au/Sn reflow soldering, and included amplifiers for up to 100 channels, signal processing units, an RF transmitter, and a power receiving and clock recovery module. An under bump metallization (UBM) using potentially biocompatible materials was developed and optimized, which consisted of a sputter deposited Ti/Pt/Au thin film stack with layer thicknesses of 50/150/150 nm, respectively. After flip-chip bonding, an underfiller was applied between the IC and the UEA to improve mechanical stability and prevent fluid ingress in in vivo conditions. A planar power receiving coil fabricated by patterning electroplated gold films on polyimide substrates was connected to the IC by using a custom metallized ceramic spacer and SnCu reflow soldering. The SnCu soldering was also used to assemble SMD capacitors on the UEA. The mechanical properties and stability of the optimized interconnections between the UEA and the IC and SMD components were measured. Measurements included the tape tests to evaluate UBM adhesion, shear testing between the Au/Sn solder bumps and the substrate, and accelerated lifetime testing of the long-term stability for the underfiller material coated with a a-SiCx:H by PECVD, which was intended as a device encapsulation layer. The materials and processes used to generate the integrated neural interface device were found to yield a robust and reliable integrated package.