Composite Finite Elements for Elliptic Boundary Value Problems with Discontinuous Coefficients

In this paper, we will introduce composite finite elements for solving elliptic boundary value problems with discontinuous coefficients. The focus is on problems where the geometry of the interfaces between the smooth regions of the coefficients is very complicated. On the other hand, efficient numerical methods such as, e.g., multigrid methods, wavelets, extrapolation, are based on a multi-scale discretization of the problem. In standard finite element methods, the grids have to resolve the structure of the discontinuous coefficients. Thus, straightforward coarse scale discretizations of problems with complicated coefficient jumps are not obvious. In this paper, we define composite finite elements for problems with discontinuous coefficients. These finite elements allow the coarsening of finite element spaces independently of the structure of the discontinuous coefficients. Thus, the multigrid method can be applied to solve the linear system on the fine scale. We focus on the construction of the composite finite elements and the efficient, hierarchical realization of the intergrid transfer operators. Finally, we present some numerical results for the multigrid method based on the composite finite elements (CFE-MG

HyperImage – Image-Oriented e-Science Networks

Images are an important source of scientific knowledge in many disciplines. E.g. you want to analyse satellite photographs or x-ray images of human livers or symbols of death in Dutch baroque paintings. You study the relevant images closely and compare details of one image with details of another. When you want to share your knowledge you will necessarily also communicate about image details. Using paper images, you can just mark up details of interest with a pencil. But with digital images you either have to make marks by employing an image manipulation software, which is not as widespread and easy to use as current text processing software is. Or you have to describe your findings verbally, such as "... above left is an interesting dark spot in picture No. 1 ... now compare it to picture No. 2 where a similar dark spot can be found nearly in the centre of the picture ..." and so on. Neither the employment of a complex image manipulation software package nor the time consuming and not very precise verbal description is satisfactory and appropriate for everyday use in science. Additionally, any technical solution to the lack of easy-to-use technology has to be Web-based in order to support collaborative research on images. The HyperImage project is concerned with the currently unsolved technical problem of establishing links between image details. Our goal is to develop a Web-based workspace that will enable scientists in any image-oriented discipline to create simple and precise links between images and image details, in a fashion similar to that which until now has been the privilege of text. The HyperImage editor permits scientists to mark details of pictures and create links between images and image details of any scale. It is programmed as a platform independent Java application and is open source (GNU Lesser General Public Licence). Any work in progress can be stored within the Hyper- Image system by an author or group of authors, or it can be exported as XML for further usage outside the HyperImage system. Currently we are testing our software prototype with our HyperImage partners from the faculties of Art History and Biology

Analyzing the higher order structure of proteins with conformer-selective ultraviolet photodissociation

The top-down approach in protein sequencing requires simple methods in which the analyte can be readily dissociated at every position along the backbone. In this context, ultraviolet photodissociation (UVPD) recently emerged as a promising tool because, in contrast to slow heating techniques such as collision induced dissociation (CID), the absorption of UV light is followed by a rather statistically distributed cleavage of backbone bonds. As a result, nearly complete sequence coverage can be obtained. It is well-known, however, that gas-phase proteins can adopt a variety of different, sometimes coexisting conformations and the influence of this structural diversity on the UVPD fragmentation behavior is not clear. Using ion mobility-UVPD-mass spectrometry we recently showed that UVPD is sensitive to the higher order structure of gas-phase proteins. In particular, the cis/trans isomerization of certain proline peptide bonds was shown to significantly influence the UVPD fragmentation pattern of two extended conformers of 11+ ubiquitin. Building on these results, we here provide conformer-selective UVPD data for 7+ ubiquitin ions, which are known to be present in a much more diverse and wider ensemble of different structures, ranging from very compact to highly extended species. Our data show that certain conformers fall into groups with similar UVPD fragmentation pattern. Surprisingly, however, the conformers within each group can differ tremendously in their collision cross section. This indicates that the multiple coexisting conformations typically observed for 7+ ubiquitin are caused by a few, not easily inter-convertible, subpopulations

Repulsion-Phase Linkage Analysis of Tetraploid Creeping Bentgrass (Agrostis Stolonifera L.)

Creeping bentgrass is a cool-season grass species primarily used on golf course greens, tees, and fairways because of its tolerance of low mowing heights and recuperative ability. Creeping bentgrass is tetraploid and outcrossing and has been characterized as having bivalent chromosome pairing through cytogenetic analysis (Jones, 1956) and disomic inheritance based on the inheritance of isozyme markers (Warnke et al., 1998). The objective of this experiment was to evaluate the extent of repulsion-phase linkages of single dose AFLP type markers in a creeping bentgrass mapping population and to infer chromosome pairing behaviour based on the ratio of coupling to repulsion-phase linkages

A long-term "memory" of HIF induction in response to chronic mild decreased oxygen after oxygen normalization

Background Endothelial dysfunction (ED) is functionally characterized by decreased vasorelaxation, increased thrombosis, increased inflammation, and altered angiogenic potential, has been intimately associated with the progression and severity of cardiovascular disease. Patients with compromised cardiac function oftentimes have a state of chronic mild decreased oxygen at the level of the vasculature and organs, which has been shown to exacerbate ED. Hypoxia inducible factor (HIF) is a transcription factor complex shown to be the master regulator of the cellular response to decreased oxygen levels and many HIF target genes have been shown to be associated with ED. Methods Human endothelial and aortic smooth muscle cells were exposed either to A) normoxia (21% O2) for three weeks, or to B) mild decreased oxygen (15% O2) for three weeks to mimic blood oxygen levels in patients with heart failure, or to C) mild decreased oxygen for two weeks followed by one week of normoxia ("memory" treatment). Levels of HIF signaling genes (HIF-1α, HIF-2α, VEGF, BNIP3, GLUT-1, PAI-1 and iNOS) were measured both at the protein and mRNA levels. Results It was found that chronic exposure to mild decreased oxygen resulted in significantly increased HIF signaling. There was also a "memory" of HIF-1α and HIF target gene induction when oxygen levels were normalized for one week, and this "memory" could be interrupted by adding a small molecule HIF inhibitor to the last week of normalized oxygen. Finally, levels of ubiquitylated HIF-1α were reduced in response to chronic mild decreased oxygen and were not full restored after oxygen normalization. Conclusion These data suggest that HIF signaling may be contributing to the pathogenesis of endothelial dysfunction and that normalization of oxygen levels may not be enough to reduce vascular stress

Photodissociation of Conformer-Selected Ubiquitin Ions Reveals Site-Specific Cis/Trans Isomerization of Proline Peptide Bonds

Ultraviolet photodissociation (UVPD) of gas-phase proteins has attracted increased attention in recent years. This growing interest is largely based on the fact that, in contrast to slow heating techniques such as collision induced dissociation (CID), the cleavage propensity after absorption of UV light is distributed over the entire protein sequence, which can lead to a very high sequence coverage as required in typical top-down proteomics applications. However, in the gas phase, proteins can adopt a multitude of distinct and sometimes coexisting conformations, and it is not clear how this three-dimensional structure affects the UVPD fragmentation behavior. Using ion mobility–UVPD–mass spectrometry in conjunction with molecular dynamics simulations, we provide the first experimental evidence that UVPD is sensitive to the higher order structure of gas-phase proteins. Distinct UVPD spectra were obtained for different extended conformations of 11+ ubiquitin ions. Assignment of the fragments showed that the majority of differences arise from cis/trans isomerization of one particular proline peptide bond. Seen from a broader perspective, these data highlight the potential of UVPD to be used for the structural analysis of proteins in the gas phas

From Compact to String—The Role of Secondary and Tertiary Structure in Charge-Induced Unzipping of Gas-Phase Proteins

In the gas phase, protein ions can adopt a broad range of structures, which have been investigated extensively in the past using ion mobility-mass spectrometry (IM-MS)-based methods. Compact ions with low number of charges undergo a Coulomb-driven transition to partially folded species when the charge increases, and finally form extended structures with presumably little or no defined structure when the charge state is high. However, with respect to the secondary structure, IM-MS methods are essentially blind. Infrared (IR) spectroscopy, on the other hand, is sensitive to such structural details and there is increasing evidence that helices as well as β-sheet-like structures can exist in the gas phase, especially for ions in low charge states. Very recently, we showed that also the fully extended form of highly charged protein ions can adopt a distinct type of secondary structure that features a characteristic C5-type hydrogen bond pattern. Here we use a combination of IM-MS and IR spectroscopy to further investigate the influence of the initial, native conformation on the formation of these structures. Our results indicate that when intramolecular Coulomb-repulsion is large enough to overcome the stabilization energies of the genuine secondary structure, all proteins, regardless of their sequence or native conformation, form C5-type hydrogen bond structures. Furthermore, our results suggest that in highly charged proteins the positioning of charges along the sequence is only marginally influenced by the basicity of individual residues

Consistency of QTL for Dollar Spot Resistance Between Greenhouse and Field Inoculations, Multiple Locations, and Different Population Sizes in Creeping Bentgrass

Dollar spot caused by Sclerotinia homoeocarpa F. T. Bennett is the most economically important turf disease in North America. Previous work indicated differences among cultivars in their susceptibility to dollar spot (Bonos et al., 2003). Studies have indicated that dollar spot resistance might be quantitatively inherited (Bonos et al., 2003) but the number, location and effect of genomic regions conferring resistance is still not known. Therefore the objective of this research is to understand the effect of population size, inoculation assays, and field locations on QTL for dollar spot resistance in creeping bentgrass