| 1. |
- Andersson, Maria, 1975, et al.
(författare)
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Differential global gene expression response patterns of human endothelium exposed to shear stress and intraluminal pressure
- 2005
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Ingår i: J Vasc Res. - : S. Karger AG. - 1018-1172. ; 42:5, s. 441-52
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the global gene expression response of endothelium exposed to shear stress and intraluminal pressure and tested the hypothesis that the two biomechanical forces induce a differential gene expression response pattern. Intact living human conduit vessels (umbilical veins) were exposed to normal or high intraluminal pressure, or to low or high shear stress in combination with a physiological level of the other force in a unique vascular ex vivo perfusion system. Gene expression profiling was performed by the Affymetrix microarray technology on endothelial cells isolated from stimulated vessels. Biomechanical forces were found to regulate a very large number of genes in the vascular endothelium. In this study, 1,825 genes were responsive to mechanical forces, which corresponds to 17% of the expressed genes. Among pressure-responsive genes, 647 genes were upregulated and 519 genes were down regulated, and of shear stress-responsive genes, 133 genes were upregulated and 771 down regulated. The fraction of genes that responded to both pressure and shear stimulation was surprisingly low, only 13% of the regulated genes. Our results indicate that the two different stimuli induce distinct gene expression response patterns, which can also be observed when studying functional groups. Considering the low number of overlapping genes, we suggest that the endothelial cells can distinguish between shear stress and pressure stimulation.
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| 2. |
- Andrienko, Gennady, et al.
(författare)
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Space, time and visual analytics
- 2010
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Ingår i: INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE. - : Taylor and Francis. - 1365-8816 .- 1362-3087. ; 24:10, s. 1577-1600
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Tidskriftsartikel (refereegranskat)abstract
- Visual analytics aims to combine the strengths of human and electronic data processing. Visualisation, whereby humans and computers cooperate through graphics, is the means through which this is achieved. Seamless and sophisticated synergies are required for analysing spatio-temporal data and solving spatio-temporal problems. In modern society, spatio-temporal analysis is not solely the business of professional analysts. Many citizens need or would be interested in undertaking analysis of information in time and space. Researchers should find approaches to deal with the complexities of the current data and problems and find ways to make analytical tools accessible and usable for the broad community of potential users to support spatio-temporal thinking and contribute to solving a large range of problems.
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| 3. |
- Bergh, Niklas, 1979, et al.
(författare)
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A new biomechanical perfusion system for ex vivo study of small biological intact vessels
- 2005
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Ingår i: Ann Biomed Eng. - : Springer Science and Business Media LLC. - 0090-6964. ; 33:12, s. 1808-18
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Tidskriftsartikel (refereegranskat)abstract
- The vascular endothelium transduces physical stimuli within the circulation into physiological responses, which influence vascular remodelling and tissue homeostasis. Therefore, a new computerized biomechanical ex vivo perfusion system was developed, in which small intact vessels can be perfused under well-defined biomechanical forces. The system enables monitoring and regulation of vessel lumen diameter, shear stress, mean pressure, variable pulsatile pressure and flow profile, and diastolic reversal flow. Vessel lumen measuring technique is based on detection of the amount of flourescein over a vessel segment. A combination of flow resistances, on/off switches, and capacitances creates a wide range of pulsatile pressures and flow profiles. Accuracy of the diameter measurement was evaluated. The diameters of umbilical arteries were measured and compared with direct ultrasonographic measurement of the vessel diameter. As part of the validation the pulsatile pressure waveform was altered, e.g., in terms of pulse pressure, frequency, diastolic shape, and diastolic reversal flow. In a series of simulation experiments, the hemodynamic homeostasis functions of the system were successfully challenged by generating a wide range of vascular diameters in artificial and intact human vessels. We conclude that the system presented may serve as a methodological and technical platform when performing advanced hemodynamic stimulation protocols.
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| 4. |
- Doroudi, Roya, 1967, et al.
(författare)
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Methodological studies of multiple reference genes as endogenous controls in vascular gene expression studies
- 2005
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Ingår i: Endothelium. - : Informa UK Limited. - 1062-3329 .- 1029-2373. ; 12:5-6, s. 215-23
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Tidskriftsartikel (refereegranskat)abstract
- Detection and quantification of differentially expressed genes requires valid and reliable references to control for error variability introduced by preparatory procedures or efficiency of reverse transcription and polymerase chain reaction (PCR) amplification conditions. So-called housekeeping genes are frequently used as endogenous standards, based on the assumption that they are constitutively expressed and independent of experimental conditions. However, if the influence of experimental stimuli is to be analyzed, it cannot a priori be assumed that their expression is unaffected by stimulation. In the present study, the authors studied the expression of different housekeeping genes in the vascular endothelium of intact conduit vessels perfused in a unique biomechanical perfusion model. Ten control gene candidates were investigated by microarray expression analysis. Further, five of these genes were systematically analyzed by real-time reverse transcriptase (RT)-PCR gene quantification and their suitability as reference genes were evaluated. On the basis of these findings, the authors suggest criteria for evaluation of endogenous control genes in vascular perfusion studies.
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| 5. |
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| 6. |
- Franks, P. W., et al.
(författare)
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Technological readiness and implementation of genomic-driven precision medicine for complex diseases
- 2021
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Ingår i: Journal of Internal Medicine. - : Wiley. - 0954-6820 .- 1365-2796. ; 290:3, s. 602-620
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Forskningsöversikt (refereegranskat)abstract
- The fields of human genetics and genomics have generated considerable knowledge about the mechanistic basis of many diseases. Genomic approaches to diagnosis, prognostication, prevention and treatment - genomic-driven precision medicine (GDPM) - may help optimize medical practice. Here, we provide a comprehensive review of GDPM of complex diseases across major medical specialties. We focus on technological readiness: how rapidly a test can be implemented into health care. Although these areas of medicine are diverse, key similarities exist across almost all areas. Many medical areas have, within their standards of care, at least one GDPM test for a genetic variant of strong effect that aids the identification/diagnosis of a more homogeneous subset within a larger disease group or identifies a subset with different therapeutic requirements. However, for almost all complex diseases, the majority of patients do not carry established single-gene mutations with large effects. Thus, research is underway that seeks to determine the polygenic basis of many complex diseases. Nevertheless, most complex diseases are caused by the interplay of genetic, behavioural and environmental risk factors, which will likely necessitate models for prediction and diagnosis that incorporate genetic and non-genetic data.
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| 7. |
- Ho, Quan, 1975-, et al.
(författare)
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A Web-Enabled Visualization Toolkit for Geovisual Analytics
- 2012
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Ingår i: Information Visualization. - : Sage Publications. - 1473-8716 .- 1473-8724. ; 11:1, s. 22-42
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Tidskriftsartikel (refereegranskat)abstract
- A framework and class library (GAV Flash) implemented in Adobe’s ActionScript is introduced, designed with the intention to significantly shorten the time and effort needed to develop customized web-enabled applications for geovisual analytics tasks. Through an atomic layered component architecture, GAV Flash provides a collection of interactive geo- and information visualization representations for exploring high dimensional spaces and extended with motion behavior. Versatile interaction methods are drawn from many data visualization research areas and optimized for dynamic web visualization of spatio-temporal and multivariate data. Based on layered component thinking and the use of programming interface mechanism the GAV Flash architecture is open and facilitates the creation of new or improved versions of existing components so that ideas can be tried out or optimized rapidly in a fully functional environment. Not only is GAV Flash a tool for interactive visualization but also supports storytelling around visual analytics in which visual representations not only serve as a discovery tool for individuals but also as a mean to share stories among users fostering a social style of collaborative data analysis. A mechanism “snapshot” for saving the explorative results of a reasoning process is introduced that aids collaboration and publication of gained insight and knowledge embedded as dynamic visualizations in blogs or web pages with associative metadata or “storytelling”.
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| 8. |
- Ho, Quan, 1975-, et al.
(författare)
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A Web-Enabled Visualization Toolkit for Geovisual Analytics
- 2011
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Ingår i: Proceedings of SPIE, the International Society for Optical Engineering. - SPIE, Bellingham WA, ETATS-UNIS : SPIE - International Society for Optical Engineering. - 9780819484055 ; , s. 78680R-78680R-12
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Konferensbidrag (refereegranskat)abstract
- We introduce a framework and class library (GAV Flash) implemented in Adobe’s ActionScript, designed with the intention to significantly shorten the time and effort needed to develop customized web-enabled applications for visual analytics or geovisual analytics tasks. Through an atomic layered component architecture, GAV Flash provides a collection of common geo- and information visualization representations extended with motion behavior including scatter matrix, extended parallel coordinates, table lens, choropleth map and treemap, integrated in a multiple, time-linked layout. Versatile interaction methods are drawn from many data visualization research areas and optimized for dynamic web visualization of spatio-temporal and multivariate data. Based on layered component thinking and the use of programming interface mechanism the GAV Flash architecture is open and facilitates the creation of new or improved versions of existing components so that ideas can be tried out or optimized rapidly in a fully functional environment. Following the Visual Analytics mantra, a mechanism “snapshot” for saving the explorative results of a reasoning process is developed that aids collaboration and publication of gained insight and knowledge embedded as dynamic visualizations in blogs or web pages with associative metadata or “storytelling”.
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| 9. |
- Ho, Quan, 1975-
(författare)
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Architecture and Applications of a Geovisual Analytics Framework
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The large and ever-increasing amounts of multi-dimensional, multivariate, multi-source, spatio-temporal data represent a major challenge for the future. The need to analyse and make decisions based on these data streams, often in time-critical situations, demands integrated, automatic and sophisticated interactive tools that aid the user to manage, process, visualize and interact with large data spaces. The rise of `Web 2.0', which is undisputedly linked with developments such as blogs, wikis and social networking, and the internet usage explosion in the last decade represent another challenge for adapting these tools to the Internet to reach a broader user community. In this context, the research presented in this thesis introduces an effective web-enabled geovisual analytics framework implemented, applied and verified in Adobe Flash ActionScript and HTML5/JavaScript. It has been developed based on the principles behind Visual Analytics and designed to significantly reduce the time and effort needed to develop customized web-enabled applications for geovisual analytics tasks and to bring the benefits of visual analytics to the public. The framework has been developed based on a component architecture and includes a wide range of visualization techniques enhanced with various interaction techniques and interactive features to support better data exploration and analysis. The importance of multiple coordinated and linked views is emphasized and a number of effective techniques for linking views are introduced.Research has so far focused more on tools that explore and present data while tools that support capturing and sharing gained insight have not received the same attention. Therefore, this is one of the focuses of the research presented in this thesis. A snapshot technique is introduced, which supports capturing discoveries made during the exploratory data analysis process and can be used for sharing gained knowledge.The thesis also presents a number of applications developed to verify the usability and the overall performance of the framework for the visualization, exploration and analysis of data in different domains. Four application scenarios are presented introducing (1) the synergies among information visualization methods, geovisualization methods and volume data visualization methods for the exploration and correlation of spatio-temporal ocean data, (2) effective techniques for the visualization, exploration and analysis of self-organizing network data, (3) effective flow visualization techniques applied to the analysis of time-varying spatial interaction data such as migration data, commuting data and trade flow data, and (4) effective techniques for the visualization, exploration and analysis of flood data.
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| 10. |
- Ho, Quan, 1975-, et al.
(författare)
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Exploratory 3D Geovisual Analytics
- 2008
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Ingår i: 2008 IEEE International Conference on Research, Innovation and Vision for the Future in Computing Communications Technologies,2008. - P. O. Box 1331, 445 Hoes Lane, Piscataway, NJ 08855-1331 USA : IEEE Operations Center. - 9781424423798 ; , s. 276-283
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Konferensbidrag (refereegranskat)abstract
- In this paper, we extend our generic -GeoAnalytics- visualization (GAV) component toolkit, based on the principles behind Visual Analytics (VA), to also support time-oriented, geographically referenced and multivariate attribute volumetric data. GAV includes components that support a mixture of technologies from the three data visualization fields: information visualization (InfoVis), geovisualization (GeoVis) and scientific visualization (SciVis). Our research concentrates on visual user interface (VUI) techniques through dynamic and direct data manipulation that permit the visual analytical process to become more interactive and focused. This paper encourages synergies between well-known information- and volume data visualization methods applied in a multiple-linked and coordinated views interface. We address challenges for improved data interaction techniques with volumetric data and the need for immediate response. Varieties of explorative data analysis (EDA) tasks and the possibility to view the information simultaneously from different perspectives and scenarios are discussed. The effectiveness of our geovisual analytics framework is demonstrated in a tailor-made volume data explorer (VDE) application that integrates InfoVis, GeoVis and SciVis visualization methods assembled from GAV components. VDE facilitates dynamic exploration and correlation of temporal ocean space temperature and salinity data supplied in a NetCDF format from NOAA. This real-world phenomenon that corresponds to a huge volumetric data set comprises more than 31 million values for a time period of 12 months in 1994.
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