| 1. |
- Hoffman, Johan, et al.
(författare)
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A General Galerkin Finite Element Method for the Compressible Euler Equations
- 2008
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Ingår i: SIAM Journal on Scientific Computing. - 1064-8275 .- 1095-7197.
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we present a General Galerkin (G2) method for the compressible Euler equations, including turbulent ow. The G2 method presented in this paper is a nite element method with linear approximation in space and time, with componentwise stabilization in the form of streamline diusion and shock-capturing modi cations. The method conserves mass, momentum and energy, and we prove an a posteriori version of the 2nd Law of thermodynamics for the method. We illustrate the method for a laminar shock tube problem for which there exists an exact analytical solution, and also for a turbulent flow problem
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| 2. |
- Algesten, Grete, et al.
(författare)
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Organic carbon budget for the Gulf of Bothnia
- 2006
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Ingår i: Journal of Marine Systems. - : Elsevier BV. - 0924-7963 .- 1879-1573. ; 63:3-4, s. 155-161
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Tidskriftsartikel (refereegranskat)abstract
- We calculated input of organic carbon to the unproductive, brackish water basin of the Gulf of Bothnia from rivers, point sources and the atmosphere. We also calculated the net exchange of organic carbon between the Gulf of Bothnia and the adjacent marine system, the Baltic Proper. We compared the input with sinks for organic carbon; permanent incorporation in sediments and mineralization and subsequent evasion of CO2 to the atmosphere. The major fluxes were riverine input (1500 Gg C year(-1)), exchange with the Baltic Proper (depending on which of several possible DOC concentration differences between the basins that was used in the calculation, the flux varied between an outflow of 466 and an input of 950 Gg C year(-1)), sediment burial (1100 Gg C year) and evasion to the atmosphere (3610 Gg C year(-1)). The largest single net flux was the emission of CO2 to the atmosphere, mainly caused by bacterial mineralization of organic carbon. Input and output did not match in our budget which we ascribe uncertainties in the calculation of the exchange of organic carbon between the Gulf of Bothnia and the Baltic Proper, and the fact that CO2 emission, which in our calculation represented 1 year (2002) may have been overestimated in comparison with long-term means. We conclude that net heterotrophy of the Gulf of Bothnia was due to input of organic carbon from both the catchment and from the Baltic Proper and that the future degree of net heterotrophy will be sensible to both catchment export of organic carbon and to the ongoing eutrophication of the Baltic Proper.
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| 3. |
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| 4. |
- Bergström, Per, 1980, et al.
(författare)
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Inventering, metodutveckling och modellering i marin miljö i Marstrandsskärgården
- 2009
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Länsstyrelsen i Västra Götalands län uppdrog år 2007 åt Institutionen för Marin ekologi att med stöd av Marbipp-verktyget dels inventera grundområdena i Marstrandsskärgården i Kungälvs kommun dels utveckla/utvärdera olika inventeringsmetoder i grunda områden. År 2008 erhölls ett tilläggsuppdrag avseende arbete med habitatmodellering med data från 2007 och från nya inventeringar genomförda år 2008 av länsstyrelsen. Inventeringen har dels utförts med småbåt och vattenkikare på sedvanligt vis, dessutom har punkter slumpats ut i området till grund för en efterföljande modellering. En ny metod med transekter och avläsning med hjälp av ekolod har också prövats. Med stöd från resultat från inventeringarna och information om bland annat vågexponering är det möjligt att klassificera olika bottenhabitat enligt det europeiska systemet för habitatklassificering EUNIS (European Nature Information System). Denna klassificering har efter modellering av substrat och vegetation i icke inventerade områden genomförts för hela undersökningsområdet. Modelleringen utfördes på två separata dataset, ett innehållande inventeringsinformation från punktlokaler (dyk, bottenhugg, droppvideo och vattenkikare) samt ett med information från inventeringar över större ytor (vattenkikare och ekolodsmätningar). Modelleringen visar på att Marstrandsområdet domineras av vegetationsfria lerbottnar (A5.3) följt av moderat exponerade infralittorala hårdbottnar (A3.2) och makrofyt dominerade sublittorala sediment. I modellen som baseras på punktlokaler dominerar mjukbottnarna helt, medan i den andra modellen är det jämnare fördelat mellan mjukbottnarna och de infralittorala hårdbottnarna.
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| 5. |
- Berntsson, Lars-Olof, et al.
(författare)
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EAST-ADL 2.0 Specification
- 2008
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Rapport (refereegranskat)abstract
- This specification of the EAST ADL 2.0 is based on the EAST-ADL developed in the EAST EEA projectand has been further refined and harmonized with on-going modelling appraches in the automotiveindustry. It presents the modeling infrastructure, i.e. how the modeling elements should be represented inthe language and the UML representation. For each package a usage example is provided.The EAST-ADL 2.0 is harmonized with AUTOSAR.The metamodel and UML profile of EAST ADL 2.0 is defined in two steps: A domain (automotive)metamodel is defined, capturing only the domain specific needs of the language, without adding the UML2details. The basic concepts of UML are used for this purpose, such as classes, compositions andassociations. Based on the domain metamodel, a UML2 profile for the domain metamodel is defined,specifying stereotypes with properties and constraints.Comments on the content of this document are welcomed, and should be directed to .Please download the latest available specification and the XMI file ready for use in UML2 tools from the website.
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| 6. |
- Bresell, Anders, et al.
(författare)
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Bioinformatic and enzymatic characterization of the MAPEG superfamily
- 2005
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Ingår i: The FEBS Journal. - : Wiley. - 1742-464X .- 1742-4658. ; 272:7, s. 1688-1703
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Tidskriftsartikel (refereegranskat)abstract
- The membrane associated proteins in eicosanoid and glutathione metabolism (MAPEG) superfamily includes structurally related membrane proteins with diverse functions of widespread origin. A total of 136 proteins belonging to the MAPEG superfamily were found in database and genome screenings. The members were found in prokaryotes and eukaryotes, but not in any archaeal organism. Multiple sequence alignments and calculations of evolutionary trees revealed a clear subdivision of the eukaryotic MAPEG members, corresponding to the six families of microsomal glutathione transferases (MGST) 1, 2 and 3, leukotriene C4 synthase (LTC4), 5-lipoxygenase activating protein (FLAP), and prostaglandin E synthase. Prokaryotes contain at least two distinct potential ancestral subfamilies, of which one is unique, whereas the other most closely resembles enzymes that belong to the MGST2/FLAP/LTC4 synthase families. The insect members are most similar to MGST1/prostaglandin E synthase. With the new data available, we observe that fish enzymes are present in all six families, showing an early origin for MAPEG family differentiation. Thus, the evolutionary origins and relationships of the MAPEG superfamily can be defined, including distinct sequence patterns characteristic for each of the subfamilies. We have further investigated and functionally characterized representative gene products from Escherichia coli, Synechocystis sp., Arabidopsis thaliana and Drosophila melanogaster, and the fish liver enzyme, purified from pike (Esox lucius). Protein overexpression and enzyme activity analysis demonstrated that all proteins catalyzed the conjugation of 1-chloro-2,4-dinitrobenzene with reduced glutathione. The E. coli protein displayed glutathione transferase activity of 0.11 µmol·min−1·mg−1 in the membrane fraction from bacteria overexpressing the protein. Partial purification of the Synechocystis sp. protein yielded an enzyme of the expected molecular mass and an N-terminal amino acid sequence that was at least 50% pure, with a specific activity towards 1-chloro-2,4-dinitrobenzene of 11 µmol·min−1·mg−1. Yeast microsomes expressing the Arabidopsis enzyme showed an activity of 0.02 µmol·min−1·mg−1, whereas the Drosophila enzyme expressed in E. coli was highly active at 3.6 µmol·min−1·mg−1. The purified pike enzyme is the most active MGST described so far with a specific activity of 285 µmol·min−1·mg−1. Drosophila and pike enzymes also displayed glutathione peroxidase activity towards cumene hydroperoxide (0.4 and 2.2 µmol·min−1·mg−1, respectively). Glutathione transferase activity can thus be regarded as a common denominator for a majority of MAPEG members throughout the kingdoms of life whereas glutathione peroxidase activity occurs in representatives from the MGST1, 2 and 3 and PGES subfamilies.
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| 7. |
- Brännström, Mattias, et al.
(författare)
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Rear end collision mitigation system for an automotive vehicle : patent pending
- 2006
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Patent (populärvet., debatt m.m.)abstract
- The present invention relates to a system (1) and method for autonomous rear impact mitigation in a host vehicle (2) having a brake system (4) and a steering system (5). The relative motion parameters between the host vehicle (2) and a second vehicle (11) behind the host vehicle (2) are established. While the host vehicle (2) has a positive velocity, the brake system (4) of the host vehicle (2) is selectively activated based on the determined relative motion parameters.
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| 8. |
- Bylesjö, Max, et al.
(författare)
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Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen
- 2009
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 8:1, s. 199-210
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Tidskriftsartikel (refereegranskat)abstract
- Tree biotechnology will soon reach a mature state where it will influence the overall supply of fiber, energy and wood products. We are now ready to make the transition from identifying candidate genes, controlling important biological processes, to discovering the detailed molecular function of these genes on a broader, more holistic, systems biology level. In this paper, a strategy is outlined for informative data generation and integrated modeling of systematic changes in transcript, protein and metabolite profiles measured from hybrid aspen samples. The aim is to study characteristics of common changes in relation to genotype-specific perturbations affecting the lignin biosynthesis and growth. We show that a considerable part of the systematic effects in the system can be tracked across all platforms and that the approach has a high potential value in functional characterization of candidate genes.
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| 9. |
- Bylesjö, Max, et al.
(författare)
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LAMINA : a tool for rapid quantification of leaf size and shape parameters
- 2008
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Ingår i: BMC Plant Biology. - : BMC. - 1471-2229. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background: An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. Such fields require measurement of large collections of leaves, with resulting conclusions being highly influenced by the accuracy of the phenotypic measurement process.Results: We have developed LAMINA (Leaf shApe deterMINAtion), a new tool for the automated analysis of images of leaves. LAMINA has been designed to provide classical indicators of leaf shape (blade dimensions) and size (area), which are typically required for correlation analysis to biomass productivity, as well as measures that indicate asymmetry in leaf shape, leaf serration traits, and measures of herbivory damage (missing leaf area). In order to allow Principal Component Analysis (PCA) to be performed, the location of a chosen number of equally spaced boundary coordinates can optionally be returned.Conclusion: We demonstrate the use of the software on a set of 500 scanned images, each containing multiple leaves, collected from a common garden experiment containing 116 clones of Populus tremula (European trembling aspen) that are being used for association mapping, as well as examples of leaves from other species. We show that the software provides an efficient and accurate means of analysing leaf area in large datasets in an automated or semi-automated work flow.
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| 10. |
- Bylesjö, Max, et al.
(författare)
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MASQOT : a method for cDNA microarray spot quality control.
- 2005
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 6, s. 250-
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundcDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.ResultsA novel methodology for cDNA microarray spot quality control is outlined. Multivariate discriminant analysis was used to assess spot quality based on existing and novel descriptors. The presented methodology displays high reproducibility and was found superior in identifying unreliable data compared to other evaluated methodologies.ConclusionThe proposed methodology for cDNA microarray spot quality control generates non-discrete values of spot quality which can be utilized as weights in subsequent analysis procedures as well as to discard spots of undesired quality using the suggested threshold values. The MASQOT approach provides a consistent assessment of spot quality and can be considered an alternative to the labor-intensive manual quality assessment process.
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