| 1. |
- Bylesjö, Max, et al.
(author)
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Orthogonal projections to latent structures as a strategy for microarray data normalization
- 2007
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In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 8:207
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Journal article (peer-reviewed)abstract
- BackgroundDuring generation of microarray data, various forms of systematic biases are frequently introduced which limits accuracy and precision of the results. In order to properly estimate biological effects, these biases must be identified and discarded.ResultsWe introduce a normalization strategy for multi-channel microarray data based on orthogonal projections to latent structures (OPLS); a multivariate regression method. The effect of applying the normalization methodology on single-channel Affymetrix data as well as dual-channel cDNA data is illustrated. We provide a parallel comparison to a wide range of commonly employed normalization methods with diverse properties and strengths based on sensitivity and specificity from external (spike-in) controls. On the illustrated data sets, the OPLS normalization strategy exhibits leading average true negative and true positive rates in comparison to other evaluated methods.ConclusionsThe OPLS methodology identifies joint variation within biological samples to enable the removal of sources of variation that are non-correlated (orthogonal) to the within-sample variation. This ensures that structured variation related to the underlying biological samples is separated from the remaining, bias-related sources of systematic variation. As a consequence, the methodology does not require any explicit knowledge regarding the presence or characteristics of certain biases. Furthermore, there is no underlying assumption that the majority of elements should be non-differentially expressed, making it applicable to specialized boutique arrays.
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| 2. |
- De Angelis, Hernán, 1974-
(author)
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Palaeo-ice streams in the north-eastern Laurentide Ice Sheet
- 2007
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Doctoral thesis (other academic/artistic)abstract
- This thesis presents a palaeoglaciological study aimed to determine the location, geometry and temporal evolution of palaeo-ice streams of the north-easternmost Laurentide Ice Sheet. The work was accomplished through the geomorphological interpretation of satellite imagery over 3.19 x 106 km2 of the Canadian Arctic, using a glaciological inversion scheme. Ice streams were active in this region during most of the time between the Last Glacial Maximum and the last deglaciation. A web of ice streams and inter-ice stream areas existed. Three major ice stream networks are identified: the M'Clintock Channel, Gulf of Boothia – Lancaster Sound and Hudson Strait. The M'Clintock Channel bears the most complex landform record, comprising three generations of palaeo-ice streams. Their location was weakly controlled by the subglacial topography and their geometry was determined by frozen-bed portions of the ice sheet, thus providing evidence for pure ice streams in the Laurentide Ice Sheet. In contrast, the more pronounced relief of the Gulf of Boothia – Lancaster Sound corridor supported topographically controlled ice streams. The landform record on emerged land along Hudson Strait is insufficient to support the existence of ice streams. It is therefore proposed that ice streams were constrained within the deep parts of the strait while flanked by cold-based zones on the margins. Small transient ice streams on Baffin and Prince of Wales islands drained local remnant ice caps during the collapse of the ice sheet. Analysis of the controls on the location and flow of palaeo-ice streams suggests that the interaction between the subglacial topography and thermal state of the substrate plays a more fundamental role than the geology. It is concluded that the behaviour of ice streams cannot be explained in terms of environmental controls alone, but the complex dynamics of ice stream shear margins and onset zones must be considered.
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| 3. |
- Efsing, Pål, 1965-, et al.
(author)
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IGSCC DISPOSITION CURVES FOR ALLOY 82 IN BWR NORMAL WATER CHEMISTRY
- 2007
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In: 13th International Conference on Environmental Degradation of Materials in Nuclear Power Systems. - 9781605600598 - 9781605600598 ; , s. 1353-1363
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Conference paper (other academic/artistic)abstract
- In many nuclear power plants, areas of susceptible material in the reactor systems are replaced or mitigated. Many of the areas where the nickel-based weld metal Alloy 182 have been used, are not replaceable but need to be mitigated. One possibility to mitigate is to make known susceptible material non-accessible for the reactor coolant water by covering it with less susceptible materials. One such possibility that has been utilized frequently in the Swedish Boiling Water Reactor (BWR) fleet is in-lay welding of butt welds in the main circulation and feed water loops with the less susceptible Alloy 82, which has fewer reported failure cases under these conditions. The study focuses on the development of a Factor of Improvement between Alloy 182 and the replacement, Alloy 82 material. As part of this, a disposition curve under conditions relevant for Normal Water Chemistry, NWC, in the Swedish BWRs is presented.
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| 4. |
- Goodfellow, Bradley, et al.
(author)
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Relict non-glacial surfaces in formerly glaciated landscapes: dynamic landform systems?
- 2007
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In: Geophysical Research Abstracts.
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Conference paper (peer-reviewed)abstract
- Relict non-glacial surfaces occur within many formerly glaciated landscapes and containimportant information on past surface processes and long-term landscape evolution(Goodfellow, 2007). While cosmogenic dating has confirmed the antiquity ofrelict non-glacial surfaces, the processes that contribute to their evolution and, consequently,the time scales over which they develop remain poorly understood. Of particularimportance is the possibility that relict non-glacial surfaces may provide geomorphicmarkers for the reconstruction of preglacial landscapes, which would allowsubsequent glacial erosion to be quantified. Furthermore, relict non-glacial surfacesmay also hold information on preglacial and interglacial environmental conditions.An investigation of relict non-glacial surfaces was undertaken through remote sensing,mapping and analysis of surfaces in a GIS, and regolith studies involving cosmogenicdating-, grain size-, X-ray diffraction-, and X-ray fluorescence analyses. Onthe basis of these on-going studies, we show that depending on spatial variables suchas bedrock lithology, slope, regolith thickness, and the abundance of fine matrix andwater some surfaces are denuding very slowly, while others display more rapid denudation.High spatial variability in denudation rates results in changing surface morphologiesover time. Rather than being static preglacial remnants, relict non-glacialsurfaces are dynamic features that have evolved during the Quaternary. While reconstructionsof preglacial landscapes and subsequent quantifications of glacial erosionfrom relict non-glacial surfaces remain valid, the Quaternary evolution of these surfacesshould also be considered.Goodfellow B.W., 2007. Relict non-glacial surfaces in formerly glaciated landscapes.Earth-Science Reviews, 80(1-2): 47-73.
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| 5. |
- Goodfellow, Bradley, et al.
(author)
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Relict non-glacial surfaces in formerly glaciated landscapes: dynamic landform systems?
- 2007
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In: Quaternary International.
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Conference paper (peer-reviewed)abstract
- Relict non-glacial surfaces occur within many formerly glaciated landscapesand contain important information on past surface processes and long-term landscape evolution. While cosmogenic dating has confirmedthe antiquity of relict non-glacial surfaces, the processes that contribute to their evolution and, consequently, the time scales over which they develop remain poorly understood. Of particular importanceis the possibility that relict non-glacial surfaces may provide geomorphic markers for the reconstruction of preglacial landscapes, which would allow subsequent glacial erosion to be quantified. Furthermore,relict non-glacial surfaces may also hold information on preglacialand interglacial environmental conditions. An investigation of relict non-glacial surfaces was undertaken through remote sensing, mapping and analysis of surfaces in a GIS, and regolith studies involvingcosmogenic dating-, grain size-, X-ray diffraction-, and X-ray fluorescenceanalyses. On the basis of these on-going studies, we show that depending on spatial variables such as bedrock lithology, slope, regolith thickness, and the abundance of fine matrix and water some surfaces are denuding very slowly, while others display more rapid denudation. High spatial variability in denudation rates results in changing surface morphologies over time. Rather than being static preglacialremnants, relict non-glacial surfaces are dynamic features that have evolved during the Quaternary. While reconstructions of preglaciallandscapes and subsequent quantifications of glacial erosion from relict non-glacial surfaces remain valid, the Quaternary evolution of these surfaces should also be considered.
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| 6. |
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| 7. |
- Ingvarsson, Johan, et al.
(author)
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Design of recombinant antibody microarrays for serum protein profiling: Targeting of complement proteins
- 2007
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 6:9, s. 3527-3536
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Journal article (peer-reviewed)abstract
- Antibody-based microarrays is a novel technology with great promise for high-throughput proteomics. The process of designing high-performing arrays has, however, turned out to be challenging. Here, we have designed the next generation of a human recombinant scFv antibody microarray platform for protein expression profiling of nonfractionated biotinylated human plasma and serum proteomes. The setup, based on black polymer Maxisorb slides interfaced with a fluorescent-based read-out system, was found to provide specific, sensitive (subpicomolar (pM) range) and reproducible means for protein profiling. Further, a chip-to-chip normalization protocol critical for comparing data generated on different chips was devised. Finally, the microarray data were found to correlate well with clinical laboratory data obtained using conventional methods, as demonstrated for a set of medium abundant (micromolar (mu M) to nanomolar (nM) range) protein analytes in serum and plasma samples derived from healthy and complement-deficient individuals.
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| 8. |
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| 9. |
- Jansson, Johan, 1973-, et al.
(author)
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The fossil fuel free future : comparing attitudes and behaviors among owners of alternative fuel vehicles and conventional vehicles
- 2007
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In: In Proceedings of the 13th Annual International Sustainable Development Research Conference (AISDRC), June 9-12, Västerås, Sweden.
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Conference paper (peer-reviewed)abstract
- The increase of passenger cars and the use of them has been identified as one cause of the increase in emissions of fossil carbon dioxide (CO2) and thus global warming. One way to slow this acceleration of emissions is to replace the current fleet of conventional vehicles (CV) running on fossil based fuels for one that is fuelled by alternative fuels (AF) such as bioethanol and/or biogas. A key stakeholder in this process is the consumer. Without consumers purchasing alternative fuel vehicles (AFV:s) and filling them up with AF:s, a decrease in the emissions fossil CO2 will be hard to achieve. The purpose of this paper is to increase the understanding of consumer attitudes and behaviors in relation to cars and fuels in a time of a possible market breakthrough of a more environmentally friendly technology. A mail-in survey was conducted on private car owners in Sweden during the winter of 2006. The sample consisted of approximately 4000 car owners, of which 1000 were owners of AFV:s, and the final response rate was close to 50%. Together with measuring attitudes and behavior towards cars and fuels, other environmentally friendly behaviors were also included, such as recycling, conserving energy and buying of organically grown food. By comparing owners of AFV:s and owners of CV:s, differences between the groups are identified and discussed. By presenting these differences, policy makers, vehicle and fuel producers, and consumers, can gain initial insights into a progressing market breakthrough for AFV:s and AF:s.
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| 10. |
- Jansson, Patrik, 1972, et al.
(author)
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Testing Properties of Generic Functions
- 2007
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In: LNCS, Proceedings of IFL 2006. ; 4449
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Conference paper (peer-reviewed)abstract
- A datatype-generic function is a family of functions indexed by (the structure of) a type. Examples include equality tests, maps and pretty printers. Property based testing tools like QuickCheck and Gast support the definition of properties and test-data generators, and they check if a monomorphic property is satisfied by the test cases. Generic functions satisfy generic properties and this paper discusses specifying and testing such properties. It shows how generic properties and generators can be expressed, and explains three bugs we found and corrected in the Generic Haskell library.
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