Munin: Browsing Doktorgradsavhandlinger (NT-fak) by Author

Display Scale in a ‘Document’ perspective : size matters

Olsen, Bernt Ivar (Doctoral thesis; Doktorgradsavhandling, 26-Nov-2012)

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Abstract:	The work summarized in this thesis has its basis in technology to support human collaboration. I have investigated how large, high-resolution display (LaHiRD) technology, implemented using display wall technology (large, tiled displays implemented as one coherent display surface) could support clinical work. Hence, I have worked with the topic of technological support for human collaboration (or –interaction) in a medical context. This thesis is three-tiered; one layer is related to how a certain novel technology, (very-) large-high-resolution displays may be of clinical use. The second layer relates to specific cognitive effects users of the novel technology may experience. The third layer relates to a novel analysis framework for sosiotechnical (STS) systems (LaHiRD technology creates STSs in use). Summarized, I found LaHiRD technology’s most prominent and interesting features to be the possibility for arbitrary sized displays and vast pixel-counts achievable. This affords a wide-range of uses, but is particularly interesting for group work situations and may enable a more ‘natural’ and embodied ‘arena’ for reasoning. In collaboration with the Radiology department at UNN an implementation of a prototype radiology interface for a Display Wall was made. A crude interface was designed, which was presented in a demo for the UNN radiologists and a couple of other invited specialists. This demo was videotaped and transcribed and the main results were extracted from these data, and others from the notes and interviews made in the design process for the radiology interface. It was found that yes: the clinicians were quite positive towards the clinical potential for technology, such as the Display Wall. Focus in future studies should be information design with more diverse and currently (visually-) unavailable information – and specific information to support the workflow and specific cognitive processes of group work-settings. Regarding the Second layer, contemporary research was at this time focusing on cognitive effects of display size. For instance: how does it affect our experience of the documents displayed that size increases? Does increasing size help our problem solving? Does increasing size help some groups of users more than others? Which tasks are affected by display size in this regard? Such questions have been posed and answered during the last decade and some of the results were intriguing for my work as well. In collaboration with Department of Psychology at UiT we found that we could try and figure out how tasks similar to those performed at a Radiology department is affected by display size. We designed an experiment to test how display size affects a spatial ability called ‘mental rotation’ (MR). Mental rotation is the task of deciding whether two images of arm-like structures, made from cubes attached face to face, are the same. This task is intuitively similar to the kind of work performed at a radiology department. ‘Objects’ (organs, body-parts, blood vessels, etc.) are viewed from different angles (‘coronal’, ‘sagittal’, ‘transverse’) and ‘healthy objects’ are compared to ‘pathological’. We designed two separate experiments. Both were a mixed design with Display Size and Angle (-of rotation between the MR stimuli objects) were within-subjects factors, while Sex was between-subjects factor. Our first study included 40 subjects of 4 groups where we alternated the two groups of males/females of which display condition they were tested first in. We presented half of the participants in the first experiment with a hypothesis stating that large displays should yield better performance, while the other half were presented with the opposite hypothesis – that smaller displays provides better performance. We found that females were indeed faster than males on the large display (but no difference in accuracy). However, the group of females who had been presented prior to the experiment with the hypothesis that large displays are better were performing significantly faster than all other three groups (females ‘believing’ that small displays are superior and both male groups). In order to strengthen this finding, or reject the hypothesis that the display size was affecting female performance (and that ‘belief’ alone was making females better), we designed a new experiment where we left out any explicit information regarding hypothesis. In the second experiment we also recruited more subjects in order to provide more evidence to our finding. We had 36 males and 32 females perform the same task as in the first experiment and we improved the research design. We used a high-speed camera to compute – and ‘control’ – a network delay in stimulus onset for the large display condition. This made within-subjects comparison in performance on small contra large display more reliable. Again we found that females significantly outperformed males in the large display condition. On average, females were about 20% faster than males in the large display condition. However, females did not perform faster on the Display Wall than on the laptop display. What we found, rather, was that males and females performed similar in the smaller laptop display condition and that the Display Wall condition had a significant detrimental effect on male performance, actually deteriorating their small-display performance by 20%. In summary, we have found that visually enlarging objects may have a detrimental effect on work-tasks that involve mental rotation of three-dimensional objects – a task that resembles the work typically performed in Radiology departments. This effect was observed with objects about twice the size of typical object sizes used in the traditional Shepard-Metzler MR task (comparing two objects at a time). As for the Third layer of this thesis, this involved establishing a document lens – processing (and ‘extracting) ‘document theory’ and developing a model – in collaboration with Documentation Studies at UiT, for systems analysis. The document model which I have assembled is comprised of 7 components: agent, means, modes, configuration, connection, construction and results (Olsen et al., 2012). This model encompasses all issues that have been a part of this thesis; the agents (Radiologists/other healthcare personnel) the technical infrastructure (means and modes; the ‘what’ and the ‘how’), the perceptual qualities of the Display Wall (how ‘larger’ may not always better – i.e. the perceptual Configuration of the document) and the social affordances (Connection) and finally – the Result (resulting document): the radiology interface (although only a crude prototype). The document model, I found, is a holistic and broad model that arguably encompass traditional ‘physical objects’ (a printed book; a contract) and all novel, digital documents. I have tried to explicate- and place this model, concept and the theory behind in relation to other ‘sociotechnical methodology’. In the Document Analysis (DA), we use the framework of traditional document analysis to try and analyse, or predict novel documents. Analysing present documents (already created), or historical documents may create a basis, or casting mould for experimental analysis. A document analysis, as presented in my work, may well have value as a communicating artefact, or Boundary Object in the requirements phase of systems development and –design, especially for sociotechnical systems where non-technical (non-functional) requirements are important. As for how to utilize DA in this context, the novel document model provides a framework and a template for document analysis.
Description:	Papers 1,2,3,4,5,6,8,9 & 10 of this thesis are not available in Munin: 1. Niels Windfeld Lund, Bernt Ivar Olsen, Otto Anshus, Tore Larsen, John Markus Bjørndalen and Gunnar Hartvigsen: '"Watch the Document on the Wall!” An Analytical Model for Health Care Documents on Large Displays', in Goos, G., Hartmanis, J. & Leeuwen, J. V. (Eds.) Lecture Notes in Computer Science, proceedings from Web Information Systems Engineering – WISE 2007 Workshops. (2007), vol. 4832/2007:395-406. Available at http://dl.acm.org/citation.cfm?id=1781545&CFID=254149216&CFTOKEN=96596662 2. Bernt Ivar Olsen, Sanjaya Babu Dhakal, Odd Petter Eldevik, Per Hasvold and Gunnar Hartvigsen: 'A large, high resolution tiled display for medical use : experiences from prototyping of a radiology scenario', Studies in health technology and informatics (2008), vol.136:535-40. Available at http://ebooks.iospress.nl/publication/11635 3. Bernt Ivar Olsen, Bruno Laeng, Kari-Ann Kristiansen and Gunnar Hartvigsen: 'Spatial tasks on a large, high-resolution tiled display : females mentally rotate large objects faster than men', In Engineering Psychology and Cognitive Ergonomics (2009), D. Harris, Springer Berlin / Heidelberg. 5639: 233-242. Available at http://link.springer.com/content/pdf/10.1007%2F978-3-642-02728-4_25 4. Bernt Ivar Olsen, Bruno Laeng, Kari-Ann Kristiansen and Gunnar Hartvigsen: 'Spatial tasks on a large, high-resolution, tiled display : a male inferiority in performance with a mental rotation task', In 'Engineering Psychology and Cognitive Ergonomics' D. Harris, Springer Berlin / Heidelberg (2011), vol. 6781:63-71. Available at http://link.springer.com/content/pdf/10.1007%2F978-3-642-21741-8_8 5. Bernt Ivar Olsen, Bruno Laeng, Kari-Ann Kristiansen and Gunnar Hartvigsen: 'Remember to Control for the (un)expected while Designing Controlled Experiments in HCI: The case of Sex Differences in the Spatial Ability of Mental Rotation and Display Size' (manuscript). 6. Bernt Ivar Olsen, Bruno Laeng, Kari-Ann Kristiansen and Gunnar Hartvigsen: 'Size does matter : females mentally rotate large objects faster than men' (manuscript) 8. Olsen, B.I., Hartvigsen, G, Lund, N.W.: 'Leaving twentiethcentury understanding of documents. From book to eBook to digital ecosystem', 4th IEEE International Conference on Digital Ecosystems and Technologies (2010), pp 600-605. Available at http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=05610589 9. Olsen, B.I., Lund, N.W., Ellingsen, G. & Hartvigsen, G: 'Document theory for the design of socio-technical systems : a document model as ontology of human expression', Journal of Documentation (2012), vol. 68(1):pp.100-126. Available at http://dx.doi.org/10.1108/00220411211200347 10. Olsen, B. I., Kristiansen, K-A., Eldevik, O. P. & Hartvigsen, G.: 'Large, high-resolution displays for co-located collaboration within healthcare : information proliferation for medical decision-making', Presented at INTERACT2009 Workshop: Team meetings within clinical domains – exploring the use of routines and technical support for communication. Uppsala, Sweden (2009).
URI:	http://hdl.handle.net/10037/4774

File(s) in this item: 2

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Characterization of sub-seabed fluid flow and hydrate systems at Nyegga, offshore mid- Norway : integration of seismic imaging and velocity modeling

Plaza-Faverola, Andreia Aletia (Doctoral thesis; Doktorgradsavhandling, 12-Nov-2010)

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Abstract:	What causes the escape of natural gases to the seafloor and how significant this escape has been along the mid-Norwegian continental margin? These are questions that guided the doctoral thesis. The thesis is part of a research project supported by the European Commission and the Norwegian Research Council, which aims at quantifying geological processes that control fluid flow and gas hydrate formation along the Norwegian-Barents-Svalbard margin. The thesis was divided in three stages according to the following three main objectives: (1) to assess the distribution of shallow gas reservoirs and paths for fluid migration from deep sources; (2) to investigate the internal structure of a vertical fluid escape feature (chimney) through implementation of high resolution travel-time reflection tomography modeling; and (3) to infer a time scale for fluid escape in the region through detailed seismic characterization of depositional settings and sediment deformation of sediments deposited during the last three major glaciations and their inter-glacial cycles. The methodology implemented consists in the integration of velocity analysis techniques and seismic imagine applied to different resolution seismic data sets. The thesis presents results from four articles that together bring us closer to the overall understanding of fluid flow related systems in Nyegga, offshore mid-Norway. While each article has separate and specific aims, the problems and results covered by the four articles are nevertheless guided by a single motive: to access geophysical and geological indications of sub-seabed fluid flow processes by the implementation of non-invasive methods. Two of the most important results encountered are first, that gas hydrates are at present hindering catastrophic escapes of fluids towards the seafloor; and second that fluid escape in the margin has seemingly been episodically. Fluid escape periods seem to be related to overpressure generation during the last three glaciations.
Description:	Paper number 1 and 2 of the thesis are not available in Munin due to publishers' restrictions: 1. Plaza-Faverola, A., S. Bünz, and J. Mienert (2010). "Fluid distributions inferred from Pwave velocity and reflection seismic amplitude anomalies beneath the Nyegga pockmark field of the mid-Norwegian margin", Marine and Petroleum Geology, 27(1): 46-60 2. Plaza-Faverola, A., G. K. Westbrook, K. Stephan, R. Exley, A. Gailler, T. Minshull and K. Broto, (2010). "Evidence from tomographic investigation of Vp variation for accumulation of substantial methane hydrate in a fluid-escape chimney in the Nyegga pockmark field, offshore Norway". JGR solid earth. v. doi:10.1029/2009JB007078, in press.
URI:	http://hdl.handle.net/10037/2812

File(s) in this item: 3

paper-3.pdf (1.402Mb)

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thesis.pdf (1.368Mb)

Geophysical characterizations of fluid flow and gas-hydrate systems of the NW-Svalbard and SW-Barents Sea margins

Rajan, Anupama (Doctoral thesis; Doktorgradsavhandling, 06-Feb-2013)

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Abstract:	The thesis consists of four parts and its four main objectives are: (1) to establish a potential link between serpentinization beneath a young sedimented-ocean ridge and carbon release and gas hydrate formation directly above it, (2) to understand the coexistence of free gas and gas-hydrate and to image the geophysical evidence for a geologically controlled gas hydrate, fluid migration pathway and seabed expulsion system, (3) to image the active fluid flow migration path-networks from deep hydrocarbon sources and to assess the distribution of shallow gas accumulation, and (4) to determine in detail the seismic velocity structure of the regions close to the landward limit of hydrate stability zone. The methodology implemented to realize this aims was achieved by integrating 3D seismic imaging, 1D velocity modeling to 2D seismic imaging and bathymetric and oceanographic data mapping. This PhD thesis presents results from four articles that glean into the fluid flow and gas-hydrate systems of the NW-Svalbard and SW-Barents Sea margins. The important results found during this research are: (1) new evidence for carbon release from the deep-seated source rock through the sediments above diapirism and methane capture in the inferred areas of serpentinization at the Knipovich Ridge, (2) new geophysical evidence for gas migration and geologically controlled gas hydrate system offshore NW-Svalbard, where several existing glacigenic debris flow units, which are spatially confined and influence gas migration pathways and hence, the location of gas leakage zones at the seafloor and (3) first findings of the formation of “tilted” bottom-simulating reflector in the SW-Barents Sea. They have formed due to variations in fluid flux along regions of deep-seated fault complexes causing a change in heat flow. The data also provides new evidence for the connection of deep-hydrocarbon and shallow gas hydrate, where existing fault complexes apparently act as pathways for the upward migration of fluids.
Description:	Papers 2, and 4 of this thesis are not available in Munin: 2. Rajan, A., J. Mienert, and S. Bünz: 'Acoustic evidence for a gas migration and release system in Arctic glaciated continental margins offshore NW-Svalbard', Marine and Petroleum Geology (2012), vol.32(1):36-49. Available at http://dx.doi.org/10.1016/j.marpetgeo.2011.12.008 3. Anupama Rajan, Stefan Bünz, Jürgen Mienert and. Andrew J. Smith: 'Tilted bottomsimulating reflectors (TBSRs) provide evidence for active fluid flow from deep hydrocarbon sources in the SW-Barents Sea' (manuscript) 4. Anupama Rajan, Tim A. Minshull and Jürgen Mienert: 'Heterogeneous distribution of gashydrate and free gas in glaciated sediments of the NW-Svalbard continental margin inferred from changes in compressional wave velocity' (manuscript).
URI:	http://hdl.handle.net/10037/5149

File(s) in this item: 2

paper_1.pdf (10.67Mb)

thesis.pdf (4.996Mb)

Relative sea level, deglaciation and tsunami history deduced from isolation basins

Romundset, Anders (Doctoral thesis; Doktorgradsavhandling, 15-Oct-2010)

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Abstract:	NORSK SAMANDRAG: Denne avhandlinga tek for seg endringane i relativt havnivå – strandforskyvinga – dei siste vel 11.500 åra på kysten av Finnmark og i midtre Hardanger. Ei stor mengd kjerneprøver frå avsettingane i innsjøar som ein gong låg under havnivået, er henta inn og analysert. Grenser mellom sediment som vart avsett i salt- eller ferskvatn er bestemt ved å analysere både kiselalgar og restar etter daude dyr og planter, og tidfest ved hjelp av radiokarbondatering. I lag med presist oppmålte høgder på innsjøtersklane, gjer desse data det mogleg å rekonstruere havnivåendringane i høg detalj. Her blir det presentert havnivåkurver som syner utviklinga i fire område; Tørvikbygd i Hardanger, Sørøya og Rolvsøya i vest-Finnmark og Nordkinnhalvøya i aust-Finnmark. Desse dokumenterer samspelet mellom landheving og havnivåstiging – stort sett har landhevinga vore sterkast, men i tida mellom ca. 9-7000 år sidan var det motsette tilfelle på finnmarkskysten – da vart fleire innsjøar atter oversvømt etter å ha lege fleire tusen år over havnivået. På Rolvsøya steig havnivået opp over ein innsjø men nådde ikkje den neste som ligg rett attmed, berre omlag 60 cm høgare. Her stabiliserte det seg i meir enn tre tusen år, fram til for ca. 5000 år sidan. Etter det har havnivået falle fleire meter fram til i dag. Ei liknande utvikling er òg funne på Sørøya og Nordkinnhalvøya, men i Tørvikbygd er historia ei anna. Her vart landet mykje hardare nedpressa mot slutten av siste istid, og landhevinga har vore tilsvarande sterk, særleg det fyrste tusenåret etter at isen forsvann – da datt strandlina gjennomsnittleg med meir enn 5 cm i året. Breen som dekte Barentshavet under siste istid, smelta vekk tidlegare enn isen over Finnmark. Dette førte til sterk heving av havbotnen som også virka inn på tidleg isfrie område av ytterkysten og medførte at spranget mellom marin grense og yngre strandliner er langt større her enn langs andre delar av norskekysten. I tillegg er bidraget til hevinga frå Barentshavet, truleg i lag med ein slakare profil på innlandsisen, årsaka til at dei heva strandlinene i Finnmark hallar mindre enn dei gjer t.d. på Vestlandet. Det er funne klåre spor etter ein tsunami i fem av innsjøane på Finnmarkskysten. Dateringar syner at dette må ha vore Storeggatsunamien, som vart utløyst av eit enormt undersjøisk skred utafor Mørekysten for om lag 8100-8200 år sidan. Bølgja slo opp i alle fall 3-4 meter i høgda, og mange hundre meter innover land. Erosjonen var sterkast nært sjøen der tsunamien grov sed ned i meir enn 3000 år eldre avleiringar. Over erosjonskontakten ligg nedst eitt sandlag, fylgd av mellom anna opprivne torvbitar og gytjeklumpar som tydeleg har rulla i sanda. Den valdsamme erosjonen og dei sorterte avsettingane tilseier at tsunamien må ha råka 17 innsjøar som ikkje var islagte, og på denne tida var klimaet vesentleg kaldare enn i dag. Dette gjer det truleg at både Storeggaskredet og tsunamien hende ein gong mellom april og oktober.
Description:	Paper number 1 of the thesis is not available in Munin due to publisher's restrictions: 1. Romundset, A., Lohne, Ø.S., Mangerud, J. & Svendsen, J.I.: «The first Holocene relative sea-level curve from the middle part of Hardangerfjorden, western Norway», Boreas 39(2010), 87-104 (Wiley). Available at http://dx.doi.org/10.1111/j.1502-3885.2009.00108.x
URI:	http://hdl.handle.net/10037/2703

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Palaeoenvironment of the Barents Sea during the last deglaciation and Holocene : processes and timing

Rüther, Denise Christina (Doctoral thesis; Doktorgradsavhandling, 01-Mar-2012)

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Abstract:	The scope of this PhD thesis is twofold: Firstly, processes, patterns and timing of the last deglaciation in the Barents Sea are reconstructed and secondly, depositional conditions on the Barents shelf during Holocene are elucidated. This cumulative PhD thesis encompasses an introductory part and five papers - three as first-author and two as co-author. Three papers are focused on the most prominent geomorphological freature of the western Barents shelf, 850 km long cross-shelf trough Bjørnøyrenna (The Bear Island Trough). One detailed study examines processes and timing of the first step of glacial retreat in outer Bjørnøyrenna and establishes a minimum age of 17 cal ka for initial deglaciation. A second study focuses on a grounding line system in uppermost Bjørnøyrenna, witnessing a surge-type readvance towards the final collapse of the marine-based Barents Sea Ice Sheet. A third study focuses on contrasting ice stream flow regimes and processes observed from glacial maximum over initial deglaciation towards final deglaciation. Two additional studies are located in the relatively small formerly glaciated trough Kveithola, north-west of Bjørnøya (Bear Island). The first focuses on the most recent deglaciation history and establishes an indirect deglaciation age for Spitsbergenbanken 14.2-13.9 cal ka ago. The other reconstructs the complex glacial retreat through Kveithola and associated processes based on geophysical data. As a whole, this PhD thesis improves existing chronology during deglaciation and Holocene for the Barents Sea, advances existing depositional models of ice-marginal and deglacial processes as well as it adds to established conceptional models of glacial retreat. While presented Holocene data is less conclusive, it might create the awareness that the large Storegga tsunami at 8.2 cal ka may have had an erosional impact on shelf sediments and thereby motivate further research.
Description:	The papers of this thesis are not available in Munin: 1. Rüther, D. C., Mattingsdal, R., Andreassen, K., Forwick, M. and Husum, K.: 'Seismic architecture and sedimentology of a major grounding zone system deposited by the Bjørnøyrenna Ice Stream during Late Weichselian deglaciation', Quaternary Science Reviews (2011) vol.30:2776-2792. Available at http://dx.doi.org/10.1016/j.quascirev.2011.06.011 2. Rüther, D. C., Bjarnadóttir, L. R. Junttila, J., Husum, K., Rasmussen, T., Lucchi, R. G. and Andreassen, K.: 'Pattern and timing of the north-western Barents Sea Ice Sheet deglaciation and indications of episodic Holocene deposition' (accepted paper in Boreas). 3. Bjarnadóttir, L. R., Rüther, D. C., Winsborrow, M. C. M. and Andreassen, K.: 'Grounding line dynamics during the last deglaciation of Kveithola, W Barents Sea, as revealed by seabed geomorphology and shallow seismic stratigraphy' (submitted manuscript to Boreas). 4. Andreassen, K., Winsborrow, M. C. M., Bjarnadóttir, L. R. and Rüther, D. C.: 'Landform assemblage from the collapse of a marine-based ice stream' (submitted manuscript to Geology). 5. Rüther, D. C., Andreassen, K. and Winsborrow, M. C. M.: 'Changing ice stream flow regimes during the last deglaciation of Bjørnøyrenna, western Barents Sea' (manuscript)
URI:	http://hdl.handle.net/10037/3876

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thesis.pdf (786.4Kb)

POP-cocktails : hangover threats for seabirds? The response of three seabird species to exposure to persistent organic pollutants in the Barents Sea

Sagerup, Kjetil (Doctoral thesis; Doktorgradsavhandling, 11-Jun-2009)

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Abstract:	The overall aim of the thesis was to study immunological effects of pollutants in Barents Sea. The Glaucous gull (Larus hyperboreus), black-legged kittiwake (Rissa tridactyla) and Atlantic puffin (Fratercula arctica) were studied. The apex predatory glaucous gull have high levels of persistent organic pollutants (POPs), while the fish eating black-legged kittiwake and Atlantic puffin are located lower in the food-chain and have lower levels of POPs. In breeding glaucous gulls, positive correlations between levels of intestinal nematode and organochlorine (OC) levels were observed. The intestinal parasite intensities could be seen as an end result of the immune system’s battle against the establishment and survival of the parasites. An increased infection with increased OC levels might be explained by immune suppression activity of OCs. The influence of the Barents Sea’s POP-cocktails on the developing immune system was studied on laboratory-raised glaucous gull chicks. The polluted group that simulated “naturally” polluted glaucous gull chicks responded less well to an influenza vaccine and had lower levels of circulating immunoglobulin-G (IgG) and IgM than the control group. The hypothesis of a POP-induced immune suppression was also investigated in the less polluted black-legged kittiwake and Atlantic puffin. The predictions of an altered level of circulating IgG with OCP, PCB or PBDE levels were tested. The results show no indication of correlations between the IgG and pollutant levels. Naturally dead glaucous gulls were studied in an attempt to evaluate whether pollutants contribute to the death. Autopsies and POP analyses reveal that the brain levels of pesticides and PCBs were the same as in a sample of dead glaucous gulls from 1989, while the liver levels were significantly lower. The brain levels thereby strengthen the theory that an additional stress provided from elevated pollutant levels could be deadly.
Description:	Papers number 1,2 and 3 of the thesis are not available in Munin due to publishers' restrictions. Paper 4 is a manuscript, and not available in Munin. 1. Sagerup, K., Henriksen, E.O., Skorping, A. Skaare, J.U., Gabrielsen G.W.: "Intensity of parasitic nematodes is associated with organochlorine levels in the glaucous gull (Larus hyperboreus)." Jornal of Applied Ecology 2000; 37: 532-239 (British Ecology Society). Available at http://dx.doi.org/10.1046/j.1365-2664.2000.00521.x 2. Sagerup, K., Larsen, H.J.S., Skaare, J.U., Johansen, G.M., Gabrielsen, G.W.: "The toxic effects of multiple persistent organic pollutant exposures on the post-hatch immunity maturation of glaucous gulls." Journal of Toxicology and Environmental Health - Part A 2009; 72: 1-14 (Taylor & Francis). Available at http://dx.doi.org/10.1080/15287390902959516 3. Sagerup, K., Savinov, V., Savinova, T., Kuklin, V.V., Muir, D.C.G., Gabrielsen, G.W.: "Persistent organic pollutants, heavy metals and parasites in the glaucous gull (Larus hyperboreus) on Spitsbergen." Environmental Pollution 2009; 157(8-9): 2282-2290 (Elsevier). Available at http://dx.doi.org/10.1016/j.envpol.2009.03.031 4. Sagerup, K., Åsbakk, K., Polder A., Skaare, J.U., Gabrielsen, G.W., Barrett, R.T.: "The effect of persistent organic pollutants (POPs) on the immune system of black-legged kittiwakes and Atlantic puffins in the Barents Sea." Manuscript.
URI:	http://hdl.handle.net/10037/2244

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Signal processing techniques for the enhancement of marine seismic data

Sanchis, Charlotte Juliette (Doctoral thesis; Doktorgradsavhandling, 12-Nov-2010)

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Abstract:

This thesis presents several signal processing techniques applied to the enhancement of marine seismic data. Marine seismic exploration provides an image of the Earth's subsurface from reflected seismic waves. Because the recorded signals are contaminated by various sources of noise, minimizing their effects with new attenuation techniques is necessary. A statistical analysis of background noise is conducted using Thomson’s multitaper spectral estimator and Parzen's amplitude density estimator. The results provide a statistical characterization of the noise which we use for the derivation of signal enhancement algorithms. Firstly, we focus on single-azimuth stacking methodologies and propose novel stacking schemes using either enhanced weighted sums or a Kalman filter. It is demonstrated that the enhanced methods yield superior results by their ability to exhibit cleaner and better defined reflected events as well as a larger number of reflections in deep waters. A comparison of the proposed stacking methods with existing ones is also discussed. We then address the problem of random noise attenuation and present an innovative application of sparse code shrinkage and independent component analysis. Sparse code shrinkage is a valuable method when a noise-free realization of the data is generated to provide data-driven shrinkages. Several models of distribution are investigated, but the normal inverse Gaussian density yields the best results. Other acceptable choices of density are discussed as well. Finally, we consider the attenuation of flow-generated nonstationary coherent noise and seismic interference noise. We suggest a multiple-input adaptive noise canceller that utilizes a normalized least mean squares alg orithm with a variable normalized step size derived as a function of instantaneous frequency. This filter attenuates the coherent noise successfully when used either by itself or in combination with a time-frequency median filter, depending on the noise spectrum and repartition along the data. Its application to seismic interference attenuation is also discussed.

URI:

http://hdl.handle.net/10037/2794

File(s) in this item: 3

thesis.pdf (30.12Mb)

thesis-sanchis-1.pdf (11.77Mb)

thesis-sanchis-2.pdf (18.49Mb)

Automatic Inspection of Cod (Gadus Morhua L.) Fillets by Hyperspectral Imaging

Sivertsen, Agnar Holten (Doctoral thesis; Doktorgradsavhandling, 11-Nov-2011)

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Abstract:	The manual trimming and inspection of cod fillets by candling, is considered the bottleneck of cod fillet processing. The operation is both labour intensive and expensive, reported to account for as much as 50 % of the cost with cod fillet production. Due to the high labour costs in Norway, it is of great interest for the industry to optimize this process. In this work a hyperspectral imaging system has been developed, capable of inspecting cod fillets, with or without skin, at a conveyor belt speed of 400 mm/seconds, corresponding to the industrial processing speed of one fish per second. The system is designed as proof of concept, and the algorithms are not implemented to be run in real time. A method for segmenting a cod fillet image into the respective parts: loin, belly and tail, using the centerline as a reference system, has been developed. The method is useful for selecting standardized measurement regions on the fillet, and used for extracting data for automatic freshness assessment. Freshness, as days on ice, can be predicted using spectroscopy in part of the visible region (450-700 nm). This can be done with an accuracy comparable to what is reported for sensory evaluation using a panel of trained evaluators. The same system is used for detecting fillets which have been previously frozen, both as whole fish and as fillets with skin. The results show a complete separation between the fresh and frozen-thawed samples. Similar mechanisms are affecting the spectra from fish stored fresh on ice, and fish that has been through the freeze-thaw cycle. The main variations seen in the spectra from cod fillets stored on ice, or frozen and then thawed, are due to oxidation of heme proteins in the muscle. This is supported by independent measurements using two different instruments, and by previous studies pointing to the visible region as the best region for freshness prediction. Detectingobjectsembeddedintissue, usingvisiblelight, isdifficultduetovariability in the optical properties of the surrounding tissue. A method for calibrating the spectral signature from small objects embedded in translucent material has been developed. This method uses the estimated local background spectrum to calibrate the hyperspectral image, and the method is evaluated for automatic nematode detection, using the hyperspectral imaging system, at a commercial cod fillet processing plant. The local calibration method is superior to using traditional spectroscopic pre-treatment methods, and reduces both spatial and spectral variations across the image. The results from the industrial test show that the system can detect nematodes in cod fillets with a performance which is comparable or better, to what is reported by manual inspection.
Description:	The papers of this thesis are not available in Munin: 1. A. H. Sivertsen, C. Chu, L. Wang, F. Godtliebsen, K. Heia and H. Nilsen: 'Ridge detection with application to automatic fish fillet inspection', Journal of Food Engineering (2009), vol. 90, pp. 317–324. Available at http://dx.doi.org/10.1016/j.jfoodeng.2008.06.035 2. A. H. Sivertsen, K. Heia, S. K. Stormo, E. Elvevoll and H. Nilsen: 'Automatic nematode detection in cod fillets (Gadus Morhua) by transillumination hyperspectral imaging', Journal of Food Science (2011), vol. 76, pp. 77-83. Available at http://dx.doi.org/10.1111/j.1750-3841.2010.01928.x 3. A. H. Sivertsen, K. Heia, K. Hindberg and F. Godtliebsen: 'Automatic nematode detection in cod fillets (Gadus Morhua L.) by hyperspectral imaging' Journal of Food Science (2011), Volume 76, Issue 1, pages S77–S8. Available at http://dx.doi.org/10.1111/j.1750-3841.2010.01928.x 4. A. H. Sivertsen, T. Kimiya and K. Heia: 'Automatic freshness assessment of cod (Gadus morhua) fillets by VIS/NIR spectroscopy', Journal of Food Engineering (2011), vol 103, pp. 317-323. Available at http://dx.doi.org/10.1016/j.jfoodeng.2010.10.030
URI:	http://hdl.handle.net/10037/3681

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Synthetic aperture ultrasound imaging with application to interior pipe inspection

Skjelvareid, Martin Hansen (Doctoral thesis; Doktorgradsavhandling, 07-Sep-2012)

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Abstract:

This thesis is concerned with synthetic aperture focusing of ultrasonic pulse-echo measurements, with application to multilayered media and cylindrical structures. The work is motivated by the need for accurate methods for non-destructive testing of pipelines, particularly water distribution pipelines. By improving the lateral resolution in ultrasonic measurements, the synthetic aperture algorithms presented in the thesis enable accurate detection and sizing of corrosion damage, holes, and other pipe defects. In ultrasonic inspection of water-filled pipelines, the water and the pipe wall constitute a multilayered structure, and multilayer synthetic aperture algorithms are therefore needed. We present a number of such multilayer algorithms, formulated in both the time and Fourier domains, and show that the Fourier-domain algorithms generally require a significantly lower processing time. An algorithm combining two algorithms used in reflection seismology is shown to require the least processing time for large data sets. When the synthetic aperture is created by scanning over a straight line or a flat plane, and the propagating medium is homogeneous, the lateral resolution after focusing is approximately half the transducer diameter. We show that this resolution limit also applies in the multilayer case, for both two- and three-dimensional imaging, as long as the transducer beam is relatively narrow. Ultrasonic measurements for pipe inspection are usually performed over a cylindrical surface. We develop a new synthetic aperture algorithm, termed cylindrical phase shift migration, to focus such scans. The algorithm is applicable to concentrically layered media, and thus enables full volumetric synthetic aperture imaging in pipes and similar structures. It is shown that the lateral resolution along the cylinder axis is approximately half the transducer diameter, and that the angular resolution is approximately D/(2R), where D denotes transducer diameter and R denotes scan radius. The algorithm is also adapted for use with focused transducers, and it is shown that it significantly extends the range within which the transducer yields a high lateral resolution.

URI:

http://hdl.handle.net/10037/4649

File(s) in this item: 1

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Theoretical studies of natural and magnetic circular dichroism

Solheim, Harald (Doctoral thesis; Doktorgradsavhandling, 23-Jun-2011)

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Abstract:	This dissertation presents theoretical studies mainly of natural and magnetic circular dichroism spectra. For magnetic circular dichroism, the importance of electron correlation effects, here included at the density-functional functional level of theory, and solvent effects are discussed, both being shown to have significant impact on the final spectra. In addition, a unified approach for calculating the temperate-independent contribution to MCD spectra are presented based on damped response theory. This approach is applicable also in energy regions with a high density of electronic states, where the calculation of MCD B terms based on residues of quadratic response functions may give unphysical results. It is argued for an abandonment of the conventional separation of the temperature-independent contribution into A and B terms since this separation may lead to incorrect analysis of the excited states. For natural circular dichroism spectra, calculations have been performed both at the electronic level, as part of a study on Vitamin B12 including calculations of absorption and magnetic circular dichroism spectra, and at the vibronic level, in both cases employing density-functional theory. The study of vibrationally resolved circular dichroism was performed for a system where the observed spectrum is solely due to isotopic substitution. The model system, 2(R)-deutoriocyclopentanone, exists in two distinct, but near isoenergetic conformations with circular dichroism signals that nearly cancel each other, emphasizing a high requirement for computational accuracy. The dissertation is concluded with a discussion on the construction of accurate model Hamiltonians for the simulation of vibronic spectra beyond the adiabatic approximation, using pyrazine as an example. Here, multireference wave-function based methods were employed in order to accurately describe potential energy surfaces over a large region of nuclear configuration space.
Description:	The papers of this thesis are not available in Munin: 1. H. Solheim, L. Frediani, K. Ruud, and S. Coriani: 'An IEF-PCM study of solvent effects on the Faraday B term of MCD', Theor. Chem. Account (2008) 119, 231. Available at http://dx.doi.org/10.1007/s00214-006-0235-9 2. H. Solheim, K. Ruud, S. Coriani, and P. Norman: 'Complex polarization propagator calculations of magnetic circular dichroism spectra', J. Chem. Phys. (2008) 128, 094103. Available at http://dx.doi.org/10.1063/1.2834924 3. H. Solheim, K. Ruud, S. Coriani, and P. Norman: 'The A and B terms of magnetic circular dichroism revisited', J. Phys. Chem A. (2008) 112, 9615. Available at http://dx.doi.org/10.1021/jp803135x 4. H. Solheim, K. Kornobis, K. Ruud, and P. M. Kozlowski: 'Electronically excited states of Vitamin B12 and methylcobalamin: Theoretical analysis of absorption, CD and MCD data', J. Phys. Chem B. (2011) 115, 737. Available at http://dx.doi.org/10.1021/jp109793r 5. Na Lin, Harald Solheim, Kenneth Ruud, Marcel Nooijen, Fabrizio Santoro, Xian Zhao, Marcin Kwit and Pawel Skowronek : 'Vibrationally resolved circular dichroism spectra of a molecule with isotopically engendered chirality', manuscript, later published in Physical Chemistry Chemical Physics, 2012, 14, 3669-3680. Published version available at http://dx.doi.org/10.1039/C2CP23584F 6. H. Solheim, A. Papp, C. Woywod, and K. Ruud: 'On the systematic construction of vibronic coupling Hamiltonians: the interaction between the 11B3u and 11B2u states of pyrazine as an example' (manuscript)
URI:	http://hdl.handle.net/10037/3591

File(s) in this item: 1

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Understanding and predicting one- and two-photon absorption properties of molecular complexes

Steindal, Arnfinn Hykkerud (Doctoral thesis; Doktorgradsavhandling, 22-Jan-2013)

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Abstract:	This thesis presents the development of theoretical models for the calculations of one- and two-photon absorption, and computational studies on solvated systems and biomolecules. The photon-absorbing chromophore is described by density functional theory, while the effects of the surroundings are taken into account by means of polarizable embedding models. The theory and implementation of a three-layered fully polarizable method is presented in this thesis. In this method, the short-range electrostatic potential due to the solvent is treated by a polarizable molecular mechanics force field, while the long-range effects are described by a dielectric continuum. This QM/MM/PCM implementation was tested on three organic molecules solvated in water and shown to converge faster with respect to system size compared to calculations using quantum mechanics/molecular mechanics (QM/MM) only. Further, the parallelization of the QM/MM module in the Dalton program is decribed, making it possible to do calculations on large molecular systems with the use of modern supercomputers. This implementation was used to calculate the one- and two-photon absorption properties in fluorescent proteins, demonstrating the importance of describing the protein surrounding the chromophore by a polarizable embedding.
Description:	The papers of this thesis are not available in Munin: 1. A. H. Steindal, K. Ruud, L. Frediani, K. Aidas and J. Kongsted: 'Excitation energies in solution: the fully polarizable QM/MM/PCM method', Journal of Physical Chemistry B (2011), vol.115(12):3027–3037. Available at http://dx.doi.org/10.1021/jp1101913 2. A. H. Steindal, J. M. H. Olsen, L. Frediani, J. Kongsted and K. Ruud: 'Parallelization of the polarizable embedding scheme for higher-order response functions', Molecular Physics (2012), Vol. 110, no.19-20. Available at http://dx.doi.org/10.1080/00268976.2012.721016 3. A. H. Steindal, J. M. H. Olsen, K. Ruud, L. Frediani and J. Kongsted: 'A combined quantum mechanics and molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein', Physical Chemistry Chemical Physics (2012), vol.14:5440-5451. Available at http://dx.doi.org/10.1039/C2CP23537D 4. M. T. P. Beerepoot, A. H. Steindal, J. M. H. Olsen, K. Ruud, L. Frediani, B. O. Brandsdal and J. Kongsted: 'A polarizable embedding DFT study of one-photon absorption in fluorescent proteins' (manuscript) 5. N. H. List, J. M. H. Olsen, H. J. Aa. Jensen, A. H. Steindal and J. Kongsted: 'Molecular-level insight into the spectral tuning mechanism of the DsRed chromophore', Journal of Physical Chemistry Letters (2012), vol.3(23):3513–3521. Available at http://dx.doi.org/10.1021/jz3014858
URI:	http://hdl.handle.net/10037/5148

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Late Glacial – Holocene climate variability and sedimentary environments on northern continental shelves Zonal and meridional Atlantic Water advection

Sørensen, Steffen Aagaard (Doctoral thesis; Doktorgradsavhandling, 22-Mar-2011)

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Abstract:	The overall objective for this PhD-study was to further advance the understanding of the oceanographic variability and development in the Nordic Seas during the Late Glacial and the Holocene and towards the present. The focus is specifically on the poleward Atlantic Water advection along the continental margins of Norway, into the SW Barents Sea and along the West Spitsbergen slope. Four high resolution sediment cores retrieved from northern continental shelve allowed examination of spatial and temporal oceanographic and environmental variability and elucidation of underlying forcing mechanisms. The sediment cores were investigated using several paleoceanographic proxies. These include planktic and benthic foraminiferal fauna distributions, measurements of stable isotopes (δ18O, δ13C) on foraminiferal tests and transfer function SST reconstructions based on planktic foraminifer species counts. Grain size analysis, IRD counts, clay mineral analysis and chemical analysis of bulk sediment carbon content were also used. Additionally the relatively new paleothermometer, the Mg/Ca-ratio, was applied on planktic and benthic foraminifera to test and examine its applicability in Subarctic and Arctic environmental settings. The Mg/Ca-ratios were used to constrain reconstructions of sea surface and bottom water temperatures. Furthermore, Mg/Ca-ratios combined with isotopic measurements performed on the same foraminiferal species were used for quantization of past oceanic salinity changes. Weak Atlantic Water influence was observed briefly at around 18,700 and after 15,000 cal yr B.P. in the SW Barents Sea indicating an early deglaciation of Ingøydjupet. Sub surface Atlantic Water inflow was observed from the beginning of the records (at 14,000 cal yr B.P.) in both the eastern Fram Strait and in Andfjorden. Atlantic Water influx was diminished during the Younger Dryas at all investigated core sites. Strong inflow of Atlantic Water resulted in emergence at the surface during the glacial – interglacial transition. The emergence had a south-north time delay of ca. 1,000 years which probably can be ascribed to increasing influence from a lingering pool of sea-ice and melt water towards the north. Reconstructed temperatures of Atlantic Water entering the Arctic Ocean through the eastern Fram Strait show a ~2°C warming during the last ca. 100 years. This warming is unprecedented over the past 2000 years and is probably linked to the Arctic amplification of global warming.
Description:	Papers 1, 2 and 5 are not available in Munin due to publishers' restrictions: 1. S. Aagaard-Sørensen, K. Husum, M. Hald, J. Knies: 'Paleoceanographic development in the SW Barents Sea during the Late WeichselianeEarly Holocene transition',Quaternary Science Reviews 29 (2010) 3442-3456. Paper available at http://dx.doi.org/10.1016/j.quascirev.2010.08.014 2. J. Junttila, S. Aagaard-Sørensen, K. Husum and M. Hald: 'Late Glacial–Holocene clay minerals elucidating glacial history in the SW Barents Sea', Marine Geology 276 (2010) 71–85. Paper available at http://dx.doi.org/10.1016/j.margeo.2010.07.009 5. Spielhagen, R. F.,Werner, K., Aagaard-Sørensen, S., Zamelczyk, K., Kandiano,E., Budeus, G., Husum, K., Marchitto, T. and Hald, M.:'Enhanced Modern Heat Transfer to the Arctic by Warm Atlantic Water', SCIENCE(2011), 331, 450-453. Paper available at http://dx.doi.org/10.1126/science.119739
URI:	http://hdl.handle.net/10037/3007

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Higher-order SCF response functions in a quasi-energy formulation

Thorvaldsen, Andreas J. (Doctoral thesis; Doktorgradsavhandling, 30-Sep-2008)

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Abstract:	This thesis is concerned with computer modelling of molecules interacting with electromagnetic radiation (light, radio waves, etc.), static electric and magnetic fields (in the laboratory), as well as approximate treatments of the motions of the molecules' atomic nuclei (vibration). Compared to interactions between electrons or between electron and nucleus, these interactions are small, and well approximated by perturbation theory. Perturbation of isolated molecules in their ground state by time-dependent electromagnetic fields is known as 'response theory' (response functions), and permits study of both ground and excited states. For the 'self-consistent field' (SCF) class of electronic structure models, which includes the popular Kohn-Sham DFT models, this thesis presents a full hierachy of new formulas for response functions. Although there are several equivalent formulas for a given response function, one specific is typically preferable due to computational considerations. The derived formulas are expressed in terms of the atomic-orbital (AO) density matrix, and take into account time- and perturbation dependence of the AOs, such as magnetic-field-dependent 'London AOs' or 'gauge-including AOs', which are employed to obtain gauge-origin independent results with improved basis set convergence. The density matrix has an advantage over the more common molecular orbital (MO) parameterization in that it typically decays rapidly with the distance between atoms. For large molecules one may therefore truncate the density matrix. This can lead to great computational savings. We formulate response theory by applying perturbation theory to 'Floquet theory' (sometimes called optical Bloch equations), which is a semi-classical quantum field theory. The central quantity in Floquet theory is the 'quasi-energy', and this is therefore the 'quasi-energy formalism' of response theory. We have implemented the response function formulas in a local version of the DALTON quantum chemistry program, and demonstrate applications to the Cotton-Mouton birefringence, coherent anti-Stokes Raman scattering, electric-field-gradient induced birefringence, and to the vibrational corrections to hyperpolarizabilities.
Description:	Papers number 2,3 and 5 of the thesis are not available in Munin due to publishers' restrictions: 2. Thorvaldsen AJ, Ferrighi L, Ruud K, Ågren H, Coriani S, Jørgensen P.:"Analytic ab initio calculations of Coherent anti-Stokes Raman Scattering (CARS)." Physical Chemistry Chemical Physics 2009; 11: 2293-2304 (Royal Society of Chemistry). Available at http://dx.doi.org/10.1039/b812045e 3. Thorvaldsen AJ, Ruud K, Jaszunski M.:"Analytic calculations of vibrational hyperpolarizabilities in the atomic orbital basis."Journal of Physical Chemistry A 2009; 356(1-3): 177-186 (Elsevier) Available at http://dx.doi.org/10.1016/j.chemphys.2008.10.033 5. Shcherbin D, Thorvaldsen AJ, Ruud K, Rizzo A, Coriani S.:" Analytical calculations of nonlinear mixed electric and magnetic frequency-dependent molecular properties using London atomic orbitals: Buckingham birefringence." Physical Chemistry Chemical Physics 2009; 11: 816-825. (Royal Society of Chemistry). Available at http://dx.doi.org/10.1039/b815752a
URI:	http://hdl.handle.net/10037/2136

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Cogset : A High-Performance MapReduce Engine

Viken Valvåg, Steffen (Doctoral thesis; Doktorgradsavhandling, 30-Jan-2012)

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Abstract:	MapReduce has become a widely employed programming model for large-scale data-intensive computations. Traditional MapReduce engines employ dynamic routing of data as a core mechanism for fault tolerance and load balancing. An alternative mechanism is static routing, which reduces the need to store temporary copies of intermediate data, but requires a tighter coupling between the components for storage and processing. The initial intuition motivating our work is that reading and writing less temporary data could improve performance, while the tight coupling of storage and processing could be leveraged to improve data locality. We therefore conjecture that a high-performance MapReduce engine can be based on static routing, while preserving the non-functional properties associated with traditional engines. To investigate this thesis, we design, implement, and experiment with Cogset, a distributed MapReduce engine that deviates considerably from the traditional design. We evaluate the performance of Cogset by comparing it to a widely used traditional MapReduce engine using a previously established benchmark. The results confirm our thesis that a high-performance MapReduce engine can be based on static routing, although analysis indicates that the reasons for Cogset's performance improvements are more subtle than expected. Through our work we develop a better understanding of static routing, its benefits and limitations, and its ramifications for a MapReduce engine. A secondary goal of our work is to explore how higher-level abstractions that are commonly built on top of MapReduce will interact with an execution engine based on static routing. Cogset is therefore designed with a generic, low-level core interface, upon which MapReduce is implemented as a relatively thin layer, as one of several supported programming interfaces. At its core, Cogset provides a few fundamental mechanisms for reliable and distributed storage of data, and parallel processing of statically partitioned data. While this dissertation mainly focuses on how these capabilities are leveraged to implement a distributed MapReduce engine, we also demonstrate how two other higher-level abstractions were built on top of Cogset. These may serve as alternative access points for data-intensive applications, and illustrate how some of the lessons learned from Cogset can be applicable in a broader context.
Description:	The papers of this thesis are not available in Munin: 1. Steffen Viken Valvåg and Dag Johansen: 'Oivos : simple and efficient distributed data processing' (2008). In Proceedings of the 2008 Tenth IEEE International Conference on High Performance Computing and Communications (HPCC 2008), pages 113– 122. IEEE Computer Society. Available at http://dx.doi.org/10.1109/HPCC.2008.105 2. Steffen Viken Valvåg and Dag Johansen: 'Update Maps : a new abstraction for High-Throughput Batch processing' (2009). In Proceedings of the 2009 IEEE International Conference on Networking, Architecture, and Storage (NAS 2009), pages 431–438. IEEE Computer Society. Available at http://dx.doi.org/10.1109/NAS.2009.73 3. Steffen Viken Valvåg and Dag Johansen: 'Cogset : a unified engine for reliable storage and parallel processing' (2009). In Proceedings of the 2009 Sixth IFIP International Conference on Network and Parallel Computing (NPC 2009), pages 174– 181. IEEE Computer Society. Available at http://dx.doi.org/10.1109/NPC.2009.23 4. Steffen Viken Valvåg, Dag Johansen, and Åge Kvalnes: 'Cogset vs. Hadoop : measurements and analysis', (2010). In Proceedings of the 2010 Second IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2010), pages 768–775. IEEE Computer Society. Available at http://dx.doi.org/10.1109/CloudCom.2010.103
URI:	http://hdl.handle.net/10037/3817

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Abstract:	Protein fosforylering er en av de viktigste intracellulære signaltransduksjonsmekanismer i eukaryote og er involvert i nesten alle cellulære prosesser. Avvikende kinase aktivitet kan forårsake mange alvorlige sykdommer som diabetes og kreft. Bruk av små molekyler for å modulere protein kinase aktivitet er nå en validert metode for behandling av slike sykdommer. Men imidlertid har kliniske studier med denne typen stoffer ofte avslørt alvorlige bivirkninger, sannsynligvis forårsaket av uspesifikke effekter på andre kinaser. Ettersom det menneskelige kinome omfatter mer enn 500 kinaser, vil en bedre forståelse av presise strukturelle mekanismer for hemmer selektivitet være et viktig hjelpemiddel i utformingen av nye legemidler.
Description:	Paper 1 and 2 of this thesis are not available in Munin: 1. Alexander Pflug, Jevgenia Rogozina, Darja Lavogina, Erki Enkvist, Asko Uri, Richard Alan Engh and Dirk Bossemeyer: 'Diversity of bisubstrate binding modes of adenosine analogue–oligoarginine conjugates in protein kinase A and implications for protein substrate interactions', Journal of Molecular Biology (2010), 403:66–77. Available at http://dx.doi.org/10.1016/j.jmb.2010.08.028 2. Alexander Pflug, Taianá Maia de Oliveira, Dirk Bossemeyer and Richard A. Engh: 'Mutants of protein kinase A that mimic the ATP-binding site of Aurora kinase', Biochemical Journal (2011), 440:85–93. Available at http://dx.doi.org/10.1042/BJ20110592
URI:	http://hdl.handle.net/10037/4145

Abstract:	To contribute to the fundamental picture of the electronic structure of low-coordinate transition metal complexes, we have carried out a series of DFT studies on mono-imido and nitrosyl complexes for different metal ions (Mn^II/III, Fe^II/III/IV, Co^II/III) and different systems of basal ligands. These studies reveal striking similarities of the electronic structure for these systems. The distinction of bent versus linear NO units is attributed to the ranking of the dz2 and dxz/yz parentage MOs relative to each other. Without a ligand trans to the NO group, the antibonding metal dz2- NO σ orbital interaction is lessened by mixing in metal pz, causing the MO to shift away from the NO ligand. This exact same orbital interaction appears to explain the existence of middle to late first-row transition metal imido complexes.
Description:	The four papers of the thesis are not available in Munin, due to publishers' restrictions: 1. Tangen, E.; Svadberg, A.; Ghosh, A. "Toward Modeling H-NOX Domains: A DFT Study of Heme-NO Complexes as Hydrogen Bond Acceptors," Inorganic Chemistry 2005, 44, 7802-7805. (American Chemical Society) Available at http://dx.doi.org/10.1021/ic050486q 2. Tangen, E.; Conradie, J.; Ghosh, A. "The Challenge of Being Straight: Explaining the Linearity of a Low-Spin {FeNO}⁷ Unit in a Tropocoronand Complex," Inorganic Chemistry 2005, 44, 8699-8706. (American Chemical Society) Available at http://dx.doi.org/10.1021/ic050781a 3. Conradie, J.; Tangen, E.; Ghosh, A. "Trigonal bipyramidal iron(III) and manganese(III) oxo, sulfido, and selenido complexes. An electronic-structural overview," Journal of Inorganic Biochemistry 2006, 100, 707-715. (Elsevier Science) Available at http://dx.doi.org/10.1016/j.jinorgbio.2006.01.029 4. Tangen, E.; Conradie, J.; Ghosh, A. "Bonding in Low-Coordinate Environments: Electronic Structure of Pseudotetrahedral Iron-Imido Complexes," J. Chem. Theory Comput. 2007, 3, 448-457. (American Chemical Society) Available at http://dx.doi.org/10.1021/ct600318n
URI:	http://hdl.handle.net/10037/1725