| 1. |
- Gamalielsson, Jonas, et al.
(författare)
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On the (lack of) robustness of gene expression data clustering
- 2004
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Ingår i: WSEAS Transactions on Biology and Biomedicine. - : World Scientific and Engineering Academy and Society. - 1109-9518 .- 2224-2902. ; 1:2, s. 198-204
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Tidskriftsartikel (refereegranskat)abstract
- We assess the robustness of partitional clustering algorithms applied to gene expression data. A number of clusterings are made with identical parameter settings and input data using SOM and k-means algorithms, which both rely on random initialisation and may produce different clusterings with different seeds. We define a reproducibility index and use it to assess the algorithms. The index is based on the number of pairs of genes consistently clustered together in different clusterings. The effect of noise applied to the original data is also studied. Our results show a lack of robustness for both classes of algorithms, with slightly higher reproducibility for SOM than for k-means.
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| 2. |
- Hamid Muhammed, Hamed, et al.
(författare)
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Semi-Automated Classification of the Physiological Condition of the Carotid Artery in 2D Ultrasound Image Sequences
- 2014
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Ingår i: WSEAS Transactions on Biology and Biomedicine. - 1109-9518 .- 2224-2902. ; 11, s. 35-44
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Tidskriftsartikel (refereegranskat)abstract
- Abstract: -A novel automated method for the classification of the physiological condition of the carotid arteryin 2D ultrasound image sequences is introduced. Unsupervised clustering was applied for the segmentationprocess in which both spatial and temporal information was utilized. Radial distension is then measured in theinner surface of the vessel wall, and this characteristic signal is extracted to reveal the detailed radial motion ofthe variable inner part of the vessel wall that is in contact with flowing blood. Characteristic differences in thistime signal were noticed among healthy young, healthy elderly and pathological elderly cases. The discreteFourier transform of the radial distension signal is then computed, and the area subtended by the transform iscalculated and utilized as a diagnostic feature. The method was tested successfully and could differentiateamong the categories of patients mentioned above. Therefore, this computer-aided method would significantlysimplify the task of medical specialists in detecting any defects in the carotid artery and thereby in detectingearly cardiovascular symptoms. The significance of the proposed method is that it is intuitive, semi-automatic,reproducible, and significantly reduces the reliance upon subjective measures.
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| 3. |
- Pham, Tuan D, et al.
(författare)
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Hidden Markov Models for Unaligned DNA Sequence Comparison
- 2005
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Ingår i: WSEAS Transactions on Biology and Biomedicine. - : World Scientific and Engineering Academy and Society (W S E A S). - 1109-9518 .- 2224-2902. ; 2, s. 64-69
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Tidskriftsartikel (refereegranskat)abstract
- Comparison of similarity between sequences can provide information for inferring the function of a newly discovered sequence, and understanding the evolutionary relationships among genes, proteins, and entire species. This paper presents a technique for computing the similarity between unaligned DNA sequences. The computation is based on the Kullback-Leibler divergence of hidden Markov models. We used the data sets taken from the threonine operons of Escherichia coli K-12 and Shigella flexneri to test the proposed method. The result obtained agrees with an alignment-based method. We further tested the proposed method with a data set of 34 complete mammalian mtDNA genomes. The phylogenetic tree derived from the second experiment shows reasonable evolutionary relationships between these species.
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| 4. |
- Tran, Dat T, et al.
(författare)
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A combined Markov and noise clustering modeling method for cell phase classification
- 2006
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Ingår i: WSEAS Transactions on Biology and Biomedicine. - : World Scientific and Engineering Academy and Society. - 1109-9518 .- 2224-2902. ; 3:3, s. 161-166
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Tidskriftsartikel (refereegranskat)abstract
- This paper proposes a classification method of cell nuclei in different mitotic phases using a combined Markov and noise clustering modeling technique. The method was tested with the data set containing 379519 cells in 892 cell sequences for 5 phases extracted from real image sequences recorded at every fifteen minutes with a time-lapse fluorescence microscopy. Experimental results showed that the proposed method performed better than the k-means modeling method.
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| 5. |
- Westermark, Pål, et al.
(författare)
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Derivation of a reversible Hill equation with modifiers affecting catalytic properties
- 2004
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Ingår i: WSEAS Transactions on Biology and Biomedicine. - 1109-9518 .- 2224-2902. ; 1, s. 91-98
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Tidskriftsartikel (refereegranskat)abstract
- An existing generic enzyme rate equation, the reversible Hill equation, was generalized to account for modifiers affecting the catalytical properties of the enzyme as well as for the case of several substrates and products. The resulting generalized reversible Hill (GRH) equation has relatively few but operationally well-defined parameters. Its usefulness is demonstrated by fitting it to experimental data on mammalian muscle phosphofructokinase. The fit is superior to that of previous models to the same data. The rate equation derived is suitable for replacing more complicated rate equations when exact mechanisms are unknown and data is scarce or contradictory.
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| 6. |
- Gårdhagen, Roland, et al.
(författare)
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Large Eddy Simulation of Stenotic Flow for Wall Shear Stress Estimation - Validation and Application
- 2011
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Ingår i: WSEAS Transactions on Biology and Biomedicine. - 1109-9518. ; 8:3, s. 86-101
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Tidskriftsartikel (refereegranskat)abstract
- Turbulent flow in the cardiovascular system may increase the risk for severe arterial disease. This workaddresses the feasibility of Large Eddy Simulation (LES) using a general purpose code as a tool for assessmentof cardiovascular flow and investigates Wall Shear Stress (WSS) in steady as well as pulsating turbulent pipeflow. Poiseuille flow was specified at the inlet, and with a suitable ammount of perturbations at the inlet it waspossible to predict experimental data. The extent of the recirculation zone was affected by the inlet disturbances,and magnitude as well as direction of the WSS vector varied significantly at the reattachment point. For thepulsating flow, WSS shows a complex pattern with different spatial and temporal variation along the pipe. Thewall shear stress gradient was calculated on the entire post-stenotic surface and each component in the gradientwas investigated. The off-diagonal components in the gradient are usually assumed to be small, but here they werefound to be on the same order of magnitude as the diagonal terms. This work demonstrates the need for a scaleresolving simulation technique to accurately model cardiovascular flows.
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| 7. |
- Gårdhagen, Roland, 1978-, et al.
(författare)
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Subject Specific Wall Shear Stress in the Human Thoracic Aorta
- 2006
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Ingår i: WSEAS Transaction on biology and biomedicine. - 1109-9518. ; 10:3, s. 609-614
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Tidskriftsartikel (refereegranskat)abstract
- Numerous studies have shown a correlation between Wall Shear Stress (WSS) and atherosclerosis, but few have evaluated the reliability of estimation methods and measures used to assessWSS, which is the subject of this work. A subject specific vessel model of the aortic arch and thoracic aorta is created fromMRI images and used for CFD simulations with MRI velocity measurements as inlet boundary condition. WSS is computed from the simulation results. Aortic WSS shows significant spatial as well as temporal variation during a cardiac cycle, which makes circumferential values very uninformative, and approximate estimates using Hagen-Poiseuille fails predict the averageWSS. Highly asymmetric flow, especially in the arch, causes the spatial WSS variations.
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| 8. |
- Kokkinakis, Dimitrios, 1965, et al.
(författare)
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Comparing Lay and Professional Language in Cardiovascular Disorders Corpora.
- 2006
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Ingår i: WSEAS Transactions on BIOLOGY and BIOMEDICINE. - 1109-9518. ; 3:6, s. 429-437
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Tidskriftsartikel (refereegranskat)abstract
- This paper reports on a corpus-based, contrastive study of Swedish medical language. It is focused on the vocabulary used in two types of medical textual material: professional portals and web-based consumer sites within the domain of cardiovascular disorders. Linguistic, statistical and quantitatively based readability studies are considered in order to find the typical language-dependent and, possibly, language independent characteristics of the material examined and suggest concrete measures that might bridge the gap in medical vocabulary as used by laypersons/consumers and professionals.
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| 9. |
- Renner, Johan, et al.
(författare)
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A method for subject specific estimation of aortic wall shear stress
- 2009
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Ingår i: WSEAS Transactions on Biology and Biomedicine. - : WSEAS Press. - 1109-9518. ; 6:3, s. 49-57
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Tidskriftsartikel (refereegranskat)abstract
- Wall shear stress (WSS) distribution in the human aorta is a highly interesting hemodynamic factor for atherosclerosis development. We present a magnetic resonance imaging (MRI) and computational fluid dynamics (CFD) based subject specific WSS estimation method and demonstrate it on a group of nine healthy volunteers (males age 23.6 ± 1.3 years). In all nine subjects, the aortic blood flow was simulated in a subject specific way, where the 3D segmented geometries and inflow profiles were obtained using MRI. No parameter settings were tailored using data from the nine subjects. Validation was performed by comparing CFD gained velocity with magnetic resonance imaging (MRI) velocity measurements. CFD and MRI velocity profiles were comparable, but the temporal variations of the differences during the cardiac cycle were significant. Spatio-temporal analyzes on the WSS distribution showed a strong subject specific influence. Subject specific models are decisive to estimate WSS distribution.
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