Lower Resolution (lower + resolution)

Distribution by Scientific Domains

Selected Abstracts

Progressive Hulls for Intersection Applications

Nikos Platis
Abstract Progressive meshes are an established tool for triangle mesh simplification. By suitably adapting the simplification process, progressive hulls can be generated which enclose the original mesh in gradually simpler, nested meshes. We couple progressive hulls with a selective refinement framework and use them in applications involving intersection queries on the mesh. We demonstrate that selectively refinable progressive hulls considerably speed up intersection queries by efficiently locating intersection points on the mesh. Concerning the progressive hull construction, we propose a new formula for assigning edge collapse priorities that significantly accelerates the simplification process, and enhance the existing algorithm with several conditions aimed at producing higher quality hulls. Using progressive hulls has the added advantage that they can be used instead of the enclosed object when a lower resolution of display can be tolerated, thus speeding up the rendering process. ACM CSS: I.3.3 Computer Graphics,Picture/Image Generation, I.3.5 Computer Graphics,Computational Geometry and Object Modeling, I.3.7 Computer Graphics,Three-Dimensional Graphics and Realism [source]

Erosion models: quality of spatial predictions

Victor Jetten
Abstract An Erratum has been published for this article in Hydrological Processes 18(3) 2004, 595. An overview is given on the predictive quality of spatially distributed runoff and erosion models. A summary is given of the results of model comparison workshops organized by the Global Change and Terrestrial Ecosystems Focus 3 programme, as well as other results obtained by individual researchers. The results concur with the generally held viewpoint in the literature that the predictive quality of distributed models is moderately good for total discharge at the outlet, and not very good for net soil loss. This is only true if extensive calibration is done: uncalibrated results are generally bad. The more simple lumped models seem to perform equally well as the more complex distributed models, although the latter produce more detailed spatially distributed results that can aid the researcher. All these results are outlet based: models are tested on lumped discharge and soil loss or on hydrographs and sedigraphs. Surprisingly few tests have been done on the comparison of simulated and modelled erosion patterns, although this may arguably be just as important in the sense of designing anti-erosion measures and determining source and sink areas. Two studies are shown in which the spatial performance of the erosion model LISEM (Limburg soil erosion model) is analysed. It seems that: (i) the model is very sensitive to the resolution (grid cell size); (ii) the spatial pattern prediction is not very good; (iii) the performance becomes better when the results are resampled to a lower resolution and (iv) the results are improved when certain processes in the model (in this case gully incision) are restricted to so called ,critical areas', selected from the digital elevation model with simple rules. The difficulties associated with calibrating and validating spatially distributed soil erosion models are, to a large extent, due to the large spatial and temporal variability of soil erosion phenomena and the uncertainty associated with the input parameter values used in models to predict these processes. They will, therefore, not be solved by constructing even more complete, and therefore more complex, models. However, the situation may be improved by using more spatial information for model calibration and validation rather than output data only and by using ,optimal' models, describing only the dominant processes operating in a given landscape. Copyright 2003 John Wiley & Sons, Ltd. [source]

Two-point dixon fat,water separation: Improving reliability and accuracy in phase correction algorithms

Maria A. Schmidt PhD
Abstract Purpose To propose an advanced phase-correction region-growing algorithm for two-point fat,water separation suitable for parotid assessment, and to evaluate the general performance of phase-correction algorithms. Materials and Methods Two region-growing algorithms were evaluated in test objects and in head images: the original phase-correction algorithm (OPC) and the advanced phase-correction algorithm with voxel size manipulation (VSM) which includes: 1) starting the region-growing process from images of lower resolution and subsequently stepping toward the original matrix size, and 2) limiting the use of low-pass filters to fat,water interfaces with partial volume effects Results Fundamental problems relate to biological tissue spectrum being poorly approximated by two discrete peaks for fat and water. The VSM algorithm was shown to be less noise-sensitive, faster, and to produce a better approximation for the field inhomogeneity map. In head images (6 volunteers, 10 slices each) 43 errors were found with the OPC algorithm and only 6 errors with the VSM algorithm. Only the OPC algorithm produced errors surrounding the parotids (10 errors). Conclusion The VSM algorithm provides a more accurate and less noise-sensitive fat,water separation. This highly significant performance improvement allows the application of phase-correction algorithms to a wider range of clinical applications. J. Magn. Reson. Imaging 2008. 2008 Wiley-Liss, Inc. [source]

Structural characterization of TiN/NbN multilayers: X-ray diffraction, energy-filtered TEM and Fresnel contrast techniques compared

Summary Two TiN/NbN multilayers with wavelength 13.6 and 6.15 nm have been characterized by X-ray diffraction (XRD), Fresnel contrast analysis (FCA) and energy-filtered transmission electron microscopy (EFTEM). Good agreement between the composition profile obtained by FCA and EFTEM is obtained if the lower resolution of the EFTEM images is taken into account. The relative advantages and disadvantages of the techniques are discussed. Used together the two TEM techniques provide a quantitative characterization that is consistent with, and for some parameters provides more precise values than, that from XRD. The analysis shows that the multilayers have narrow interfaces (< 1 nm) and a composition amplitude close to 95% for the longer wavelength. [source]

A peptide-based immunoassay for antibodies against botulinum neurotoxin A

M. Zouhair Atassi
Abstract Cervical dystonia (CD) is due to neck-muscle spasms that cause pain and involuntary contractions resulting in abnormal neck movements and posture. Symptoms can be relieved by injecting the affected muscle with a botulinum neurotoxin (BoNT, usually type A or type B). The therapeutic benefits are impermanent and toxin injections need to be repeated every 3,6 months. In a very small percentage of patients (less with BoNT/A than with BoNT/B) the treatment elicits blocking anti-toxin antibodies (Abs), which reduce or terminate the patient's responsiveness to further treatment. We have recently mapped (Dolimbek et al., 2006) the CD sera Ab-binding profile using a panel of 60, 19-residue peptides that encompassed the entire H chain sequence 449,1296 and overlapped consecutively by 5 residues. Abs in CD sera bound to one or more of the peptides N25, C10, C15, C20, and C31. This suggested the possibility that binding to these peptides could be used for assay of Abs in CD sera. Data analysis reported here found that Ab binding to these regions showed very significant deviations from the control responses. Of these four peptides, C10 showed the most significant level of separation between patient and control groups (p,=,5,,10,7) and the theoretical resolution (i.e., ability to distinguish CD patients from control, see full definition under ,Statistical analysis' in Methods), 84%, was about 4% higher than the least resolved response, C31 (p,=,6,,10,6, resolution 80%). Since the amounts of Abs bound to a given peptide varied with the patient and not all the patients necessarily recognized all four peptides, there was the possibility that binding to combinations of two or more peptides might give a better discriminatory capability. Using two peptides, C10 plus C31, the resolution improved to 87% (p,=,4,,10,8). These two peptides appeared to compliment each other and negate the lower resolution of C31. Combination of three peptides gave resolutions that ranged from 85 (N25,+,C15,+,C31; p,=,2,,10,7) to 88% (C10,+,C15,+,C31; p,=,1,,10,8). Finally, using the data of all four peptides, N25,+,C10,+,C15,+,C31, gave a resolution of 86% (p,=,1,,10,7). Although these levels of resolution are somewhat lower than that obtained with whole BoNT/A (resolution 97%; p,=,6,,10,12), it may be concluded that the two-peptide combination C10,+,C31, or the three-peptide combination C10,+,C15,+,C31 (affording resolutions of 87 and 88%, respectively) provide a good diagnostic, toxin-free procedure for assay of total specific anti-toxin Abs in BoNT/A-treated CD patients. Copyright 2006 John Wiley & Sons, Ltd. [source]

Collective Dynamics of Large Proteins from Mixed Coarse-Grained Elastic Network Model

Ozge Kurkcuoglu
Abstract Elastic network model- a coarse-grained normal mode analysis- is widely used to investigate the functionally important collective motions of proteins and their complexes. Mixed coarse-graining approach has been recently introduced to the elastic network model, so that the protein's native conformation can be modeled with regions of low and high resolution. In the mixed resolution model, each node of the elastic network may represent either a single atom (high-resolution) or a residue (low-resolution), and close-neighboring nodes are connected by harmonic springs. Here, the high-resolution parts constitute the interesting parts of the protein, such as the active site, while the rest of the structure is retained at lower resolution. By performing normal mode analysis of the resulting network, the collective dynamics (low-frequency modes) and consequent conformational changes can be analyzed even for supramolecular assemblages with reasonable computational efficiency, which may serve as a means of incorporating protein flexibility into docking algorithms and drug design. In this study, the mixed coarse-graining methodology is applied to analyze the functional motions of an important enzyme, triosephosphate isomerase. [source]

The radio expansion and brightening of the very young supernova remnant G1.9 + 0.3

D. A. Green
ABSTRACT Recent radio observations of the small Galactic supernova remnant G1.9 + 0.3 made at 4.86 GHz with the Very Large Array are presented, and compared with earlier observations at 1.49 GHz which have a comparable resolution (10 4 arcsec2). These show that the radio emission from this remnant has expanded significantly, by about 15 per cent over 23 yr, with a current outer diameter of ,92 arcsec. This expansion confirms that G1.9 + 0.3 is the youngest Galactic remnant yet identified, only about 150 yr old at most. Recent, lower resolution, 1.43-GHz observations are also discussed, and the integrated flux densities from these and the 4.86-GHz observations are compared with earlier results. This shows that the integrated flux density of G1.9 + 0.3 has been increasing recently. [source]

Mass spectrometry for the detection of differentially expressed proteins: a comparison of surface-enhanced laser desorption/ionization and capillary electrophoresis/mass spectrometry

Nils v. Neuhoff
The discovery of biomarkers is currently attracting much interest as it harbors great potential for the diagnosis and monitoring of human diseases. Here we have used two advanced mass spectroscopy based technologies, surface enhanced laser desorption ionization (SELDI-MS) and capillary electrophoresis/mass spectrometry (CE/MS), to obtain proteomic patterns of urine samples from patients suffering from membranous glomerulonephritis (MGN) and healthy volunteers. The results indicate that CE/MS analysis is able to display a rich and complex pattern of polypeptides with high resolution and high mass accuracy. In order to analyze these patterns, the MosaiqueVisu software was developed for peak identification, deconvolution and the display of refined maps in a three-dimensional format. The polypeptide profiles obtained with SELDI-MS from the same samples are much sparser and show lower resolution and mass accuracy. The SELDI-MS profiles are further heavily dependent on analyte concentration. SELDI-MS analysis identified three differentially expressed polypeptides, which are potential biomarkers that can distinguish healthy donors from patients with MGN. In contrast, approximately 200 potential biomarkers could be identified by CE/MS. Thus, while SELDI-MS is easy to use and requires very little sample, CE/MS generates much richer data sets that enable an in-depth analysis. Copyright 2003 John Wiley & Sons, Ltd. [source]

A smooth and differentiable bulk-solvent model for macromolecular diffraction

T. D. Fenn
Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute,solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, Rfree and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6,) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography. [source]

Structure of the Escherichia coli RNA polymerase , subunit C-terminal domain

Samuel Lara-Gonzlez
The , subunit C-terminal domain (,CTD) of RNA polymerase (RNAP) is a key element in transcription activation in Escherichia coli, possessing determinants responsible for the interaction of RNAP with DNA and with transcription factors. Here, the crystal structure of E. coli,CTD (, subunit residues 245,329) determined to 2.0, resolution is reported. Crystals were obtained after reductive methylation of the recombinantly expressed domain. The crystals belonged to space group P21 and possessed both pseudo-translational symmetry and pseudo-merohedral twinning. The refined coordinate model (R factor = 0.193, Rfree = 0.236) has improved geometry compared with prior lower resolution determinations of the ,CTD structure [Jeon et al. (1995), Science, 270, 1495,1497; Benoff et al. (2002), Science, 297, 1562,1566]. An extensive dimerization interface formed primarily by N- and C-terminal residues is also observed. The new coordinates will facilitate the improved modeling of ,CTD-containing multi-component complexes visualized at lower resolution using X-ray crystallography and electron-microscopy reconstruction. [source]

Multiple crystal structures of actin dimers and their implications for interactions in the actin filament

Michael R. Sawaya
The structure of actin in its monomeric form is known at high resolution, while the structure of filamentous F-actin is only understood at considerably lower resolution. Knowing precisely how the monomers of actin fit together would lead to a deeper understanding of the dynamic behavior of the actin filament. Here, a series of crystal structures of actin dimers are reported which were prepared by cross-linking in either the longitudinal or the lateral direction in the filament state. Laterally cross-linked dimers, comprised of monomers belonging to different protofilaments, are found to adopt configurations in crystals that are not related to the native structure of filamentous actin. In contrast, multiple structures of longitudinal dimers consistently reveal the same interface between monomers within a single protofilament. The reappearance of the same longitudinal interface in multiple crystal structures adds weight to arguments that the interface visualized is similar to that in actin filaments. Highly conserved atomic interactions involving residues 199,205 and 287,291 are highlighted. [source]

Applications of ACORN to data at 1.45 resolution

V. Rajakannan
One of the main interests in the molecular biosciences is in understanding structure,function relations and X-ray crystallography plays a major role in this. ACORN can be used as a comprehensive and efficient phasing procedure for the determination of protein structures when atomic resolution data are available. An initial model can automatically be built by ARP/wARP followed by REFMAC for refinement. The , helices and , sheets occurring in many protein structures can be taken as starting fragments for structure solution in ACORN. ACORN, along with ARP/wARP followed by REFMAC, can be an ab initio method for solving protein structure for which data are better than 1.2 (atomic resolution). Attempts are here made in extending its applications to real data at 1.45 resolution and also to truncated data at 1.6 resolution. Two previously known structures, congerin II and alkaline cellulase N257, were resolved using the above approach. Automatic structure solution, phasing and refinement for real data at still lower resolutions for proteins of various complexities are being carried out. Data mining of the secondary structural features using PDB is being carried out for this new approach for `seed-phasing' to ACORN. [source]

The vertical resolution sensitivity of simulated equilibrium temperature and water-vapour profiles

Abstract Variability of atmospheric water vapour is the most important climate feedback in present climate models. Thus, it is of crucial importance to understand the sensitivity of water vapour to model attributes, such as physical parametrizations and resolution. Here we attempt to determine the minimum vertical resolution necessary for accurate prediction of water vapour. To address this issue, we have run two single-column models to tropical radiative,convective equilibrium states and have examined the sensitivity of the equilibrium profiles to vertical resolution. Both column models produce reasonable equilibrium states of temperature and moisture. Convergence of the profiles was achieved in both models using a uniform vertical resolution of around 25 hPa. Coarser resolution leads to significant errors in both the water vapour and temperature profiles, with a resolution of 100 hPa proving completely inadequate. However, fixing the boundary-layer resolution and altering only the free-tropospheric resolution significantly reduces sensitivity to vertical resolution in one of the column models, in both water and temperature, highlighting the importance of resolving boundary-layer processes. Additional experiments show that the height of the simulated tropopause is sensitive to upper-tropospheric vertical resolution. At resolutions higher than 33 hPa, one of the models developed a high degree of vertical structure in the vapour profile, resulting directly from the complex array of microphysical processes included in the stratiform cloud parametrization, some of which were only resolved at high resolutions. This structure was completely absent at lower resolutions, casting some doubt on the approach of using relatively complicated cloud schemes at low vertical resolutions. [source]

Inclusion of weak high-resolution X-ray data for improvement of a group II intron structure

Jimin Wang
It is common to report the resolution of a macromolecular structure with the highest resolution shell having an averaged I/,(I) , 2. Data beyond the resolution thus defined are weak and often poorly measured. The exclusion of these weak data may improve the apparent statistics and also leads to claims of lower resolutions that give some leniency in the acceptable quality of refined models. However, the inclusion of these data can provide additional strong constraints on atomic models during structure refinement and thus help to correct errors in the original models, as has recently been demonstrated for a protein structure. Here, an improved group II intron structure is reported arising from the inclusion of these data, which helped to define more accurate solvent models for density modification during experimental phasing steps. With the improved resolution and accuracy of the experimental phases, extensive revisions were made to the original models such that the correct tertiary interactions of the group II intron that are essential for understanding the chemistry of this ribozyme could be described. [source]