| 1. |
- Godhe, Anna, 1967, et al.
(författare)
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Intercalibration of classical and molecular techniques for identification of Alexandrium fundyense (Dinophyceae) and estimation of cell densities
- 2007
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Ingår i: Harmful Algae. - : Elsevier BV. - 1568-9883. ; 6:1, s. 56-72
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Tidskriftsartikel (refereegranskat)abstract
- A workshop with the aim to compare classical and molecular techniques for phytoplankton enumeration took place at Kristineberg Marine Research Station, Sweden, in August 2005. Seventeen different techniques - nine classical microscopic-based and eight molecular methods - were compared. Alexandrium fundyense was the target organism in four experiments. Experiment 1 was designed to determine the range of cell densities over which the methods were applicable. Experiment 2 tested the species specificity of the methods by adding Alexandrium ostenfeldii, to samples containing A. fundyense. Experiments 3 and 4 tested the ability of the methods to detect the target organism within a natural phytoplankton community. Most of the methods could detect cells at the lowest concentration tested, 100 cells L-1, but the variance was high for methods using small volumes, such as counting chambers and slides. In general, the precision and reproducibility of the investigated methods increased with increased target cell concentration. Particularly molecular methods were exceptions in that their relative standard deviation did not vary with target cell concentration. Only two of the microscopic methods and three of the molecular methods had a significant linear relationship between their cell count estimates and the A. fundyense concentration in experiment 2, where the objective was to discriminate that species from a morphologically similar and genetically closely related species. None of the investigated methods were affected by the addition of a natural plankton community background matrix in experiment 3. The results of this study are discussed in the context of previous intercomparisons and the difficulties in defining the absolute, true target cell concentration. (c) 2006 Elsevier B.V. All rights reserved.
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| 2. |
- Salfity, M.F., et al.
(författare)
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Extending the dynamic range of phase contrast magnetic resonance velocity imaging using advanced higher-dimensional phase unwrapping algorithms
- 2006
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Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 3:8, s. 415-427
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Tidskriftsartikel (refereegranskat)abstract
- Phase contrast magnetic resonance velocity imaging is a powerful technique for quantitative in vivo blood flow measurement. Current practice normally involves restricting the sensitivity of the technique so as to avoid the problem of the measured phase being 'wrapped' onto the range - π to + π. However, as a result, dynamic range and signal-to-noise ratio are sacrificed. Alternatively, the true phase values can be estimated by a phase unwrapping process which consists of adding integral multiples of 2π to the measured wrapped phase values. In the presence of noise and data undersampling, the phase unwrapping problem becomes non-trivial. In this paper, we investigate the performance of three different phase unwrapping algorithms when applied to three-dimensional (two spatial axes and one time axis) phase contrast datasets. A simple one-dimensional temporal unwrapping algorithm, a more complex and robust three-dimensional unwrapping algorithm and a novel velocity encoding unwrapping algorithm which involves unwrapping along a fourth dimension (the 'velocity encoding' direction) are discussed, and results from the three are presented and compared. It is shown that compared to the traditional approach, both dynamic range and signal-to-noise ratio can be increased by a factor of up to five times, which demonstrates considerable promise for a possible eventual clinical implementation. The results are also of direct relevance to users of any other technique delivering time-varying two-dimensional phase images, such as dynamic speckle interferometry and synthetic aperture radar
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| 3. |
- Marklund, Olov, et al.
(författare)
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Robust unwrapping algorithm for 3-D phase volumes of arbitrary shape containing knotted phase singularity loops
- 2005
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The extension of path-independent 2-D phase unwrapping algorithms, based on placement of branch cut lines between phase singularities of opposite sign, was recently proposed for phase volumes in a recent paper by Huntley. In 3-D the singularities were shown to form closed loops and path-independence was achieved by placing branch cut surfaces across the loops. In the current paper we describe in detail an optimised and extended version of Huntley's algorithm. This deals in particular with two aspects which are essential for practical phase volumes: (1) how to close partial loops which pass through arbitrary boundaries separating valid and invalid phase data, and (2) how to select the set of loops having shortest length. The second algorithm is necessary to deal with the ambiguous cases that can arise when the singularities form knots, i.e. two loops pass through a single phase volume element. The perfomance of the algorithm is demonstrated on 3-D phase maps from two types of medical imaging data: MRI and x-ray interferometry.
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| 4. |
- Sukuru, Sai Chetan K, et al.
(författare)
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Discovering new classes of Brugia malayi asparaginyl-tRNA synthetase inhibitors and relating specificity to conformational change.
- 2006
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Ingår i: Journal of computer-aided molecular design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 20:3, s. 159-78
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Tidskriftsartikel (refereegranskat)abstract
- SLIDE software, which models the flexibility of protein and ligand side chains while docking, was used to screen several large databases to identify inhibitors of Brugia malayi asparaginyl-tRNA synthetase (AsnRS), a target for anti-parasitic drug design. Seven classes of compounds identified by SLIDE were confirmed as micromolar inhibitors of the enzyme. Analogs of one of these classes of inhibitors, the long side-chain variolins, cannot bind to the adenosyl pocket of the closed conformation of AsnRS due to steric clashes, though the short side-chain variolins identified by SLIDE apparently bind isosterically with adenosine. We hypothesized that an open conformation of the motif 2 loop also permits the long side-chain variolins to bind in the adenosine pocket and that their selectivity for Brugia relative to human AsnRS can be explained by differences in the sequence and conformation of this loop. Loop flexibility sampling using Rigidity Optimized Conformational Kinetics (ROCK) confirms this possibility, while scoring of the relative affinities of the different ligands by SLIDE correlates well with the compounds' ranks in inhibition assays. Combining ROCK and SLIDE provides a promising approach for exploiting conformational flexibility in structure-based screening and design of species selective inhibitors.
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