Proteomics identification of differentially expressed proteins in the muscle of dysferlin myopathy patients

The muscular dystrophies are a large and heterogeneous group of neuromuscular disorders that can be classified according to the mode of inheritance, the clinical phenotype and the molecular defect. To better understand the pathological mechanisms of dysferlin myopathy we compared the protein-expression pattern in the muscle biopsies of six patients with this disease with six patients with limb girdle muscular dystrophy 2A, five with facioscapulohumeral dystrophy and six normal control subjects. To investigate differences in the expression levels of skeletal muscle proteins we used 2-DE and MS. Western blot or immunohistochemistry confirmed relevant results. The study showed specific increase expression of proteins involved in fast-to-slow fiber type conversion (ankyrin repeat protein 2), type I predominance (phosphorylated forms of slow troponin T), sarcomere stabilization (actinin-associated LIM protein), protein ubiquitination (TRIM 72) and skeletal muscle differentiation (Rho-GDP-dissociation inhibitor ly-GDI) in dysferlin myopathy. As anticipated, we also found differential expression of proteins common to all the muscular dystrophies studied. This comparative proteomic analysis suggests that in dysferlin myopathy (i) the type I fiber predominance is an active process of fiber type conversion rather than a selective loss of type II fibers and (ii) the dysregulation of proteins involved in muscle differentiation further confirms the role of dysferlin in this process.     

Annotation of multiword expressions in the Prague dependency treebank

We describe annotation of multiword expressions (MWEs) in the Prague dependency treebank, using several automatic pre-annotation steps. We use subtrees of the tectogrammatical tree structures of the Prague dependency treebank to store representations of the MWEs in the dictionary and pre-annotate following occurrences automatically. We also show a way to measure reliability of this type of annotation.     

Towards an Unbiased Comparison of CC,BCC, and FCC Lattices in Terms of Prealiasing

In the literature on optimal regular volume sampling, the Body‐Centered Cubic (BCC) lattice has been proven to be optimal for sampling spherically band‐limited signals above the Nyquist limit. On the other hand, if the sampling frequency is below the Nyquist limit, the Face‐Centered Cubic (FCC) lattice was demonstrated to be optimal in reducing the prealiasing effect. In this paper, we confirm that the FCC lattice is indeed optimal in this sense in a certain interval of the sampling frequency. By theoretically estimating the prealiasing error in a realistic range of the sampling frequency, we show that in other frequency intervals, the BCC lattice and even the traditional Cartesian Cubic (CC) lattice are expected to minimize the prealiasing. The BCC lattice is superior over the FCC lattice if the sampling frequency is not significantly below the Nyquist limit. Interestingly, if the original signal is drastically undersampled, the CC lattice is expected to provide the lowest prealiasing error. Additionally, we give a comprehensible clarification that the sampling efficiency of the FCC lattice is lower than that of the BCC lattice. Although this is a well‐known fact, the exact percentage has been erroneously reported in the literature. Furthermore, for the sake of an unbiased comparison, we propose to rotate the Marschner‐Lobb test signal such that an undue advantage is not given to either lattice.     

Optimal search path for service in the presence of disruptions

We consider the following basic search path problem: a customer residing at a node of a network needs to obtain service from one of the facilities; facility locations are known and fixed. Facilities may become inoperational with certain probability; the state of the facility only becomes known when the facility is visited. Customer travel stops when the first operational facility is found. The objective is to minimize the expected total travel distance.     

On mesh-free valley surface extraction with application to low frequency sound simulation

Crease surfaces describe extremal structures of 3D scalar fields. We present a new region-growing-based approach to the meshless extraction of adaptive nonmanifold valley and ridge surfaces that overcomes limitations of previous approaches by decoupling point seeding and triangulation of the surface. Our method is capable of extracting valley surface skeletons as connected minimum structures. As our algorithm is inherently mesh-free and curvature adaptive, it is suitable for surface construction in fields with an arbitrary neighborhood structure. As an application for insightful visualization with valley surfaces, we choose a low frequency acoustics simulation. We use our valley surface construction approach to visualize the resulting complex-valued scalar pressure field for arbitrary frequencies to identify regions of sound cancellation. This provides an expressive visualization of the topology of wave node and antinode structures in simulated acoustics.     

Visualization of myocardial perfusion derived from coronary anatomy

Visually assessing the effect of the coronary artery anatomy on the perfusion of the heart muscle in patients with coronary artery disease remains a challenging task. We explore the feasibility of visualizing this effect on perfusion using a numerical approach. We perform a computational simulation of the way blood is perfused throughout the myocardium purely based on information from a three-dimensional anatomical tomographic scan. The results are subsequently visualized using both three-dimensional visualizations and bull's eye plots, partially inspired by approaches currently common in medical practice. Our approach results in a comprehensive visualization of the coronary anatomy that compares well to visualizations commonly used for other scanning technologies. We demonstrate techniques giving detailed insight in blood supply, coronary territories and feeding coronary arteries of a selected region. We demonstrate the advantages of our approach through visualizations that show information which commonly cannot be directly observed in scanning data, such as a separate visualization of the supply from each coronary artery. We thus show that the results of a computational simulation can be effectively visualized and facilitate visually correlating these results to for example perfusion data.     

Listener-based analysis of surface importance for acoustic metrics

Acoustic quality in room acoustics is measured by well defined quantities, like definition, which can be derived from simulated impulse response filters or measured values. These take into account the intensity and phase shift of multiple reflections due to a wave front emanating from a sound source. Definition (D50) and clarity (C50) for example correspond to the fraction of the energy received in total to the energy received in the first 50 ms at a certain listener position. Unfortunately, the impulse response measured at a single point does not provide any information about the direction of reflections, and about the reflection surfaces which contribute to this measure. For the visualization of room acoustics, however, this information is very useful since it allows to discover regions with high contribution and provides insight into the influence of all reflecting surfaces to the quality measure. We use the phonon tracing method to calculate the contribution of the reflection surfaces to the impulse response for different listener positions. This data is used to compute importance values for the geometry taking a certain acoustic metric into account. To get a visual insight into the directional aspect, we map the importance to the reflecting surfaces of the geometry. This visualization indicates which parts of the surfaces need to be changed to enhance the chosen acoustic quality measure.We apply our method to the acoustic improvement of a lecture hall by means of enhancing the overall speech comprehensibility (clarity) and evaluate the results using glyphs to visualize the clarity (C50) values at listener positions throughout the room.     

Nodes on ropes: a comprehensive data and control flow for steering ensemble simulations

Flood disasters are the most common natural risk and tremendous efforts are spent to improve their simulation and management. However, simulation-based investigation of actions that can be taken in case of flood emergencies is rarely done. This is in part due to the lack of a comprehensive framework which integrates and facilitates these efforts. In this paper, we tackle several problems which are related to steering a flood simulation. One issue is related to uncertainty. We need to account for uncertain knowledge about the environment, such as levee-breach locations. Furthermore, the steering process has to reveal how these uncertainties in the boundary conditions affect the confidence in the simulation outcome. Another important problem is that the simulation setup is often hidden in a black-box. We expose system internals and show that simulation steering can be comprehensible at the same time. This is important because the domain expert needs to be able to modify the simulation setup in order to include local knowledge and experience. In the proposed solution, users steer parameter studies through the World Lines interface to account for input uncertainties. The transport of steering information to the underlying data-flow components is handled by a novel meta-flow. The meta-flow is an extension to a standard data-flow network, comprising additional nodes and ropes to abstract parameter control. The meta-flow has a visual representation to inform the user about which control operations happen. Finally, we present the idea to use the data-flow diagram itself for visualizing steering information and simulation results. We discuss a case-study in collaboration with a domain expert who proposes different actions to protect a virtual city from imminent flooding. The key to choosing the best response strategy is the ability to compare different regions of the parameter space while retaining an understanding of what is happening inside the data-flow system.     

The slope of a transfer function

Exact and approximate equations are derived that relate the magnitude slope of a general transfer function directly to its phase angle. The result is used to derive simple conditions on stabilizability of feedback loops with right half-plane poles and zeros or dead-time.     

Exploring multi-user interactions with dynamic NFC-displays

Near Field Communication (NFC) is an emerging technology for touch-based mobile interactions with single- and multi-tagged objects. Although the latter may allow for simultaneous and collaborative interactions, most prototypes were not designed for multiple users and were only evaluated with single-user interactions. In this paper, we investigate the design, usability and user experience of multi-user interactions on dynamic NFC-displays. These interactive surfaces use a grid of NFC-tags for the direct manipulation of projected application user interfaces. In two user studies with three prototypes for multi-user interaction, we evaluated the performance of dynamic NFC-displays, interactions among users and the interplay between mobile devices and large displays.