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  • 301.
    Andersson, Emma
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Metallkoncentrationer i sediment: Jämförelse mellan en fjällsjö och sjöar påverkad av gruvdrift2012Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Metal concentration (Pb,Cu, Zn and As) in alpine lake sediments in comparison to sediment affected by sulfidemining

    Many companies are prospecting for sulfide minerals in northern Sweden and mining activities in this area are likely to increase within the near future. The aim of this report was to estimate to what extent the metal concentration in lake sediments are expected to be altered by mining activities, by comparing the sediment concentrations in a pristine alpine lake sediment with that of sediment deposited in lakes near sulfide mines. Pristine lake sediments was collected from Lake Vuolep Silbbajávrre using a HTH sediment corer and analyzed using the X-ray fluorescence (XRF) while published metal concentrations from six mining lakes were used as a reference for the geochemical conditions in sulfide mining lakes. I found that sediment concentrations were typically hundred to thousand times higher in mining lakes compare to that in Vuolep Silbbajávrre. My results suggest that the metal loading in alpine lakes is expected to increase when sulfide mines are opening in Swedish sub-arctic alpine regions. The increase was especially high for As and Zn that showed the highest enrichments in the mining lakes in comparison to the alpine lake sediment. Higher concentrations of the metals are likely to have negative consequences for the benthic fauna having the sediment as habitat, considering that concentrations in the mining lakes sometimes exceed levels where negative biotic effects are expected. If the mineral exploration becomes a reality and new sulfide mines are opened in the Swedish alpine region, it will most likely result in a considerably increase in metal concentrations in nearby lakes.

  • 302.
    Andersson, Emma K.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Bengtsson, Christoffer
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Evans, Margery L.
    Chorell, Erik
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Sellstedt, Magnus
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Lindgren, Anders E.G.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hufnagel, David A.
    Bhattacharya, Moumita
    Tessier, Peter M.
    Wittung-Stafshede, Pernilla
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Chapman, Matthew R.
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). University of Michigan, USA.
    Modulation of Curli Assembly and Pellicle Biofilm Formation by Chemical and Protein Chaperones2013In: Chemistry and Biology, ISSN 1074-5521, E-ISSN 1879-1301, Vol. 20, no 10, p. 1245-1254Article in journal (Refereed)
    Abstract [en]

    Enteric bacteria assemble functional amyloid fibers, curli, on their surfaces that share structural and biochemical properties with disease-associated amyloids. Here, we test rationally designed 2-pyridone compounds for their ability to alter amyloid formation of the major curli subunit CsgA. We identified several compounds that discourage CsgA amyloid formation and several compounds that accelerate CsgA amyloid formation. The ability of inhibitor compounds to stop growing CsgA fibers was compared to the same property of the CsgA chaperone, CsgE. CsgE blocked CsgA amyloid assembly and arrested polymerization when added to actively polymerizing fibers. Additionally, CsgE and the 2-pyridone inhibitors prevented biofilm formation by Escherichia coli at the air-liquid interface of a static culture. We demonstrate that curli amyloid assembly and curli-dependent biofilm formation can be modulated not only by protein chaperones, but also by "chemical chaperones."

  • 303.
    Andersson, Emma K.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Chapman, Matthew
    Small Molecule Disruption of B-subtilis Biofilms by Targeting the Amyloid Matrix2013In: Chemistry and Biology, ISSN 1074-5521, E-ISSN 1879-1301, Vol. 20, no 1, p. 5-7Article in journal (Other academic)
    Abstract [en]

    Small molecule inhibitors of amyloid aggregation have potential as treatment for a variety of conditions. In this issue of Chemistry & Biology, Romero and colleagues use amyloid-dependent B. subtilis biofilm formation to screen for amyloid inhibitors, identifying compounds that not only inhibit B. subtilis biofilm formation but also ones that disrupt preformed biofilms.

  • 304.
    Andersson, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Modellering av säkringsstrategier för en elförsäljningsportfölj2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Because of the high volatility of the electricity spot price there is a necessity of hedging the sales price of the production. The electricity spot price are volatile and are affected by climate, producer supply and political decisions. This means that the revenues from the power activites can vary alot from one year to another. The revenues from the power activites are especially important to be able to budget with probability since they are included in the total budget of Umeå municipality. In order to evaluate possible investment strategies the production along with the electricity spot- and futures prices of different maturities are modelled together. The modelling of production and electricity spot prices are based on a general seasonal block bootstrap method. Furthermore, two different assumptions are made about the relationship between spot prices and futures prices. The first emprical model is based on an assumption that there exists a mismatch between spot prices and the futures prices and historical differences are used to calculate this. The second model is based on the assumption that the futures prices are the same as the expected future spot price and that these are consistent.

    The municipality’s current strategy is to hedge 300 GWh of the annual production in futures with three different maturities and sell the remaining of the production at spot price. This strategy can be seen as an average of four electricity prices and therefore reduces the risk of mismatch between the futures and spot price.

    The empirical study show that historically it has been most profitable to invest in futures with maturity of three years. This has to do with the historical differences between futures prices and the electricity spot prices for this maturity has been the largest and thus gives the highest expected sales profit in the model. Furthermore, the study show that it has been more profitable to invest in futures compared with selling to spot price. Whether this is something that will continue into the future is uncertain due to the nature of the futures contract and the pricing of these. Finally, the study also show which investment strategies has been most profitable in a so-called backtest.

  • 305.
    Andersson, Gabriella
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Hantering av kemikalier och dess risker i frisörverksamheter2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The purpose of this study was to examine the hairdresser’s knowledge about the chemicals they handle in their business and how they were handling the chemicals and the risks that follows. 9 Salons were visited to gather information. The same questions were asked at the salons. A sample of hair color products was photographed to gather information about ingredients and labeling. The conclusions of the study were that hairdressers have good knowledge about the risks related to human health but they need to improve their knowledge when it comes to environmental risks. The deficiencies that were found were that they lack knowledge about the laws concerning the use and distribution of cosmetics products and that not all saloons are handling the hazardous waste and residues from treatments correctly. The risks that could follow are that not enough is done to protect human health and the environmental. To prevent that damage to human health and the environmental occurs they should use more sources that focus on health and environmental to gather information about the risks with the chemicals they are handling, they should also limit the treatments on children and always inform about the risks when they are using products that can cause an allergic reaction.

    Keywords: Risks hairdressing, cosmetics products, p-phenylenediamine, Toluene-2,5-diamine, ammonia.

  • 306.
    Andersson, Göran
    et al.
    Umeå University, Faculty of Science and Technology, Physics.
    Sundqvist, Bertil
    Umeå University, Faculty of Science and Technology, Physics.
    Pressure dependence of the c-axis resistance of stage 2 SbCl5 intercalated graphite to 4 GPa1988In: Solid State Communications, ISSN 0038-1098, E-ISSN 1879-2766, Vol. 65, no 7, p. 735-738Article in journal (Refereed)
    Abstract [en]

    The c-axis electrical resistance R has been measured under pressure up to 4 GPa (40 kbar) at room temperature for stage 2, HOPG-based SbCl5 intercalated graphite. In addition to the well known ordering transition at 0.3–0.5 GPa a second anomaly in R is observed above 1 GPa, corresponding to a further phase transition which is not completed until above 2.4 GPa. In all phases R depends more strongly on p for the intercalated material than for HOPG, and the total decrease in R is over 80% to 4 GPa.

  • 307.
    Andersson, Göran
    et al.
    Umeå University, Faculty of Science and Technology, Physics.
    Sundqvist, Bertil
    Umeå University, Faculty of Science and Technology, Physics.
    Bäckström, Gunnar
    Umeå University, Faculty of Science and Technology, Physics.
    A high-pressure cell for electrical resistance measurements at hydrostatic pressures up to 8 GPa: Results for Bi, Ba, Ni, and Si1989In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 65, no 10, p. 3943-3950Article in journal (Refereed)
    Abstract [en]

    A modified Bridgman anvil high-pressure device, capable of producing hydrostatic pressures up to 8 GPa (80 kbar), was designed and built. The size of the pressure chamber (10 mm in diameter) allows the use of large specimens and simple experimental procedures. Experimental results show that hydrostatic conditions are necessary if accurate quantitative information is desired about the electrical properties of materials under pressure. Accurate data on resistance (and resistivity) versus pressure at 294 K are given for Bi, Ba, Ni, and Si. The initial pressure coefficients of R were d(ln R)dP=0.13, −7.6×10−2, −2.0×10−2, and −0.26 GPa−1, respectively. Barium has a resistance minimum near 0.9 GPa. For Bi we observe sharp transitions at 2.55, 2.7, and 7.7 GPa, and for Ba at 5.55 GPa, but we cannot verify the existence of a transition in Ba near 7 GPa. Neither do we confirm the phase transformation in Ni recently reported to occur above 2.5 GPa. For Si, R(P) agrees very well with a theoretical function calculated from the change in band gap and electron mobility with pressure.

  • 308.
    Andersson, Göran
    et al.
    Umeå University, Faculty of Science and Technology, Physics.
    Sundqvist, Bertil
    Umeå University, Faculty of Science and Technology, Physics.
    Bäckström, Gunnar
    Umeå University, Faculty of Science and Technology, Physics.
    Electrical resistivity measurements under hydrostatic conditions up to 10 GPa1984In: Journal de Physique Colloques vol. 45: Supplément C8, Physics and Physicochemistry of Highly Condensed Matter; Proceedings of the XXIInd Meeting of the EHPRG, Aussois, Sept. 1984, 1984, p. 379-382Conference paper (Refereed)
    Abstract [en]

    A large scale Bridgman anvil system has been designed. Steel gaskets permit compression of a methanol-ethanol medium over a volume of 500-250 mm3. Up to 12 wires have been used to contact specimens. The system has so far served up to 7.5 GPa, with anvils made of ASP tool steel. The transition Bi III-V was found to occur at a lower pressure than the recommended average. The electrical resistance of copper was measured up to 6 GPa under hydrostatic conditions.

  • 309.
    Andersson, Hans
    Umeå University, Faculty of Science and Technology, Chemistry.
    Reaction Between Grignard reagents and Heterocyclic N-oxides: Synthesis of Substituted Pyridines, Piperidines and Piperazines2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis describes the development of new synthetic methodologies for preparation of bioactive interesting compounds, e.g. substituted pyridines, piperidines or piparazines. Thesecompounds are synthesized from commercially available, cheap and easily prepared reagents, videlicet the reaction between Grignard reagents and heterocyclic N-oxides.

     The first part of this thesis deals with an improvement for synthesis of dienal-oximes and substituted pyridines. This was accomplished by a rapid addition of Grignard reagents to pyridine N-oxides at rt. yielding a diverse set of substituted dienal-oximes. During these studies, it was observed that the obtained dienal-oxmies are prone to ring-close upon heating. By taking advantage of this, a practical synthesis of substituted pyridines was developed.

    In the second part, an ortho-metalation of pyridine N-oxides using Grignard reagents is discussed. The method can be used for incorporation of a range of different electrophiles, including aldehydes, ketones and halogens. Furthermore, the importance for incorporation of halogens are exemplified through a Suzuki–Miyaura coupling reaction of 2-iodo pyridine N-oxides and different boronic acids. Later it was discovered that if the reaction temperature is kept below -20 °C, the undesired ringopening can be avoided. Thus, the synthesis of 2,3-dihydropyridine N-oxide, by reacting Grignard reagents with pyridine N-oxides at -40 °C followed by sequential addition of aldehyde or ketone, was accomplished. The reaction provides complete regio- and stereoselectivity yielding trans-2,3-dihydropyridine N-oxides in good yields. These intermediate products could then be used for synthesis of either substituted piperidines, by reduction, or reacted in a Diels–Alder cycloaddtion to give the aza-bicyclo compound.

    In the last part of this thesis, the discovered reactivity for pyridine N-oxides, is applied on pyrazine N-oxides in effort to synthesize substituted piperazines. These substances are obtained by the reaction of Grignard reagents and pyrazine N-oxides at -78 °C followed by reduction and protection, using a one-pot procedure. The product, a protected piperazine, that easily can be orthogonally deprotected, allowing synthetic modifications at either nitrogens in a fast and step efficient manner. Finally, an enantioselective procedure using a combination of PhMgCl and (-)-sparteine is discussed, giving opportunity for a stereoselective synthesis of substituted piperazines.

  • 310.
    Andersson, Hans
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Banchelin, Thomas Sainte-Luce
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Das, Pralay
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gustafsson, Magnus
    Acadia Pharmaceuticals AB, Medeon Science Park S-20512, Malmö, Sweden.
    Olsson, Roger
    Acadia Pharmaceuticals AB, Medeon Science Park S-20512, Malmö, Sweden.
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Complete regioselective addition of grignard reagents to pyrazine N-oxides, toward an efficient enantioselective synthesis of substituted piperazines2010In: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 12, no 2, p. 284-6Article in journal (Refereed)
    Abstract [en]

    A conceptually new one-pot strategy for the synthesis of protected substituted piperazines via the addition of Grignard reagents to pyrazine N-oxides is presented. This strategy is high yielding (33-91% over three steps), step-efficient, and fast. The synthesized N,N-diprotected piperazines are convenient to handle and allow for orthogonal deprotection at either nitrogen for selective transformations. In addition, this is a synthetic route to enantiomerically enriched piperazines by using a combination of phenyl magnesium chloride and (-)-sparteine, which resulted in enantiomeric excesses up to 83%.

  • 311.
    Andersson, Hans
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Das, Sajal
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gustafsson, Magnus
    Olsson, Roger
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Synthesis of substituted 4-pyridones and 4-aminopyridinium salts via a one-pot pyridine synthesis2010In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 51, no 32, p. 4218-4220Article in journal (Refereed)
    Abstract [en]

    Synthesis of substituted 4-benzyloxypyridinium salts by the addition of Grignard reagents to pyridine N-oxides provides an efficient route for obtaining substituted 4-pyridones or 4-aminopyridinium salts.

  • 312.
    Andersson, Hans
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gustafsson, Magnus
    Boström, Dan
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Olsson, Roger
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The Regio- and Stereoselective Synthesis of trans-2,3-Dihydropyridine N-oxides and Piperidines2009In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 48, no 18, p. 3288-3291Article in journal (Refereed)
    Abstract [en]

    No Abstract

  • 313.
    Andersson, Hans
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sainte-Luce Banchelin, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Das, Sajal
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Olsson, Roger
    Institutionen för kemi och molekylärbiologi, Göteborgs universitet, Göteborg, Sverige .
    Almqvist, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Efficient, mild and completely regioselective synthesis of substituted pyridines2010In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 46, no 19, p. 3384-3386Article in journal (Refereed)
    Abstract [en]

    Addition of Grignard reagents to pyridine N-oxides in THF at low temperature (-78 to -20 °C) and treatment with TFAA provides an efficient general procedure for synthesis of substituted pyridines. The method is compatible with a range of functional groups such as esters, halogens and nitriles.

  • 314.
    Andersson, Henrik
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Classification of spectral signatures in biological aerosols2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In this thesis multivariate methods were used to evaluate pretreatment methods, such as normalization, as well as classification possibilities of data collected with Laser Induced Breakdown Spectroscopy (LIBS). The LIBS system that FOI is currently developing for the purpose of classifying biological airborne threats was used to collect data from ten different samples in a laboratory environment. Principal component analysis (PCA) shows that it is possible to observe differences between samples using the two types of data acquired from the LIBS system, i.e., 2D CCD camera images and 1D spectra extracted from the image. Further results using partial least squares discriminant analysis (PLS-DA) show that normalization of the data only has visual effects in the PCA score-plots and do not affect the models predictability. Results also show that cropping and binning the pixels in the image is possible to some extent without losing significant predictability.

  • 315.
    Andersson, Ida E.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Modified Glycopeptides Targeting Rheumatoid Arthritis: Exploring molecular interactions in class II MHC/glycopeptide/T-cell receptor complexes2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Rheumatoid arthritis (RA) is an autoimmune inflammatory disease that leads to degradation of cartilage and bone mainly in peripheral joints. In collagen-induced arthritis (CIA), a mouse model for RA, activation of autoimmune CD4+ T cells depends on a molecular recognition system where T-cell receptors (TCRs) recognize a complex between the class II MHC Aq protein and CII259-273, a glycopeptide epitope from type II collagen (CII). Interestingly, vaccination with the Aq/CII259-273 complex can relieve symptoms and cause disease regression in mice. This thesis describes the use of modified glycopeptides to explore interactions important for binding to the Aq protein and recognition by autoimmune T-cell hybridomas obtained from mice with CIA.

    The CII259-273 glycopeptide was modified by replacement of backbone amides with different amide bond isosteres, as well as substitution of two residues that anchor the glycopeptide in prominent pockets in the Aq binding site. A three-dimensional structure of the Aq/glycopeptide complex was modeled to provide a structural basis for interpretation of the modified glycopeptide’s immunological activities. Overall, it was found that the amide bond isosteres affected Aq binding more than could be explained by the static model of the Aq/glycopeptide complex. Molecular dynamics (MD) simulations, however, revealed that the introduced amide bond isosteres substantially altered the hydrogen-bonding network formed between the N-terminal 259-265 backbone sequence of CII259-273 and Aq. These results indicated that the N-terminal hydrogen-bonding interactions follow a cooperative model, where the strength and presence of individual hydrogen bonds depended on the neighboring interactions.

    The two important anchor residues Ile260 and Phe263 were investigated using a designed library of CII259-273 based glycopeptides with substitutions by different (non-)natural amino acids at positions 260 and 263. Evaluation of binding to the Aq protein showed that there was scope for improvement in position 263 while Ile was preferred in position 260. The obtained SAR understanding provided a valuable basis for future development of modified glycopeptides with improved Aq binding. Furthermore, the modified glycopeptides elicited varying T-cell responses that generally could be correlated to their ability to bind to Aq. However, in several cases, there was a lack of correlation between Aq binding and T-cell recognition, which indicated that the interactions with the TCRs were determined by other factors, such as presentation of altered epitopes and changes in the kinetics of the TCR’s interaction with the Aq/glycopeptide complex.

    Several of the modified glycopeptides were also found to bind well to the human RA-associated DR4 protein and elicit strong responses with T-cell hybridomas obtained from transgenic mice expressing DR4 and the human CD4 co-receptor. This encourages future investigations of modified glycopeptides that can be used to further probe the MHC/glycopeptide/TCR recognition system and that also constitute potential therapeutic vaccines for treatment of RA. As a step towards this goal, three modified glycopeptides presented in this thesis have been identified as candidates for vaccination studies using the CIA mouse model.

  • 316.
    Andersson, Ida E
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Andersson, C David
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Batsalova, Tsvetelina
    Medicinal Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm.
    Dzhambazov, Balik
    Medicinal Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm.
    Holmdahl, Rikard
    Medicinal Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm.
    Kihlberg, Jan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Linusson, Anna
    AstraZeneca R&D Mölndal, Mölndal.
    Design of glycopeptides used to investigate class II MHC binding and T-Cell responses associated with autoimmune arthritis2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 3, p. e17881-Article in journal (Refereed)
    Abstract [en]

    The glycopeptide fragment CII259–273 from type II collagen (CII) binds to the murine Aq and human DR4 class II Major Histocompatibility Complex (MHC II) proteins, which are associated with development of murine collagen-induced arthritis (CIA) and rheumatoid arthritis (RA), respectively. It has been shown that CII259–273 can be used in therapeutic vaccination of CIA. This glycopeptide also elicits responses from T-cells obtained from RA patients, which indicates that it has an important role in RA as well. We now present a methodology for studies of (glyco)peptide-receptor interactions based on a combination of structure-based virtual screening, ligand-based statistical molecular design and biological evaluations. This methodology included the design of a CII259–273 glycopeptide library in which two anchor positions crucial for binding in pockets of Aq and DR4 were varied. Synthesis and biological evaluation of the designed glycopeptides provided novel structure-activity relationship (SAR) understanding of binding to Aq and DR4. Glycopeptides that retained high affinities for these MHC II proteins and induced strong responses in panels of T-cell hybridomas were also identified. An analysis of all the responses revealed groups of glycopeptides with different response patterns that are of high interest for vaccination studies in CIA. Moreover, the SAR understanding obtained in this study provides a platform for the design of second-generation glycopeptides with tuned MHC affinities and T-cell responses.

  • 317.
    Andersson, Ida E.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Batsalova, Tsvetelina
    Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet.
    Haag, Sabrina
    Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet.
    Dzhambazov, Balik
    Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet.
    Holmdahl, Rikard
    Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet.
    Kihlberg, Jan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Linusson, Anna
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    (E)-Alkene and Ethylene Isosteres Substantially Alter the Hydrogen-Bonding Network in Class II MHC Aq/Glycopeptide Complexes and Affect T-Cell Recognition2011In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 133, no 36, p. 14368-14378Article in journal (Refereed)
    Abstract [en]

    The structural basis for antigen presentation by class II major histocompatibility complex (MHC) proteins to CD4(+) T-cells is important for understanding and possibly treating autoimmune diseases. In the work described in this paper, (E)-alkene and ethylene amide-bond isosteres were used to investigate the effect of removing hydrogen-bonding possibilities from the CII259-270 glycopeptide, which is bound by the arthritis-associated murine A(q) class II MHC protein. The isostere-modified glycopeptides showed varying and unexpectedly large losses of A(q) binding that could be linked to the dynamics of the system. Molecular dynamics (MD) simulations revealed that the backbone of CII259-270 and the A(q) protein are able to form up to 11 hydrogen bonds, but fewer than this number are present at any one time. Most of the strong hydrogen-bond interactions were formed by the N-terminal part of the glycopeptide, i.e., in the region where the isosteric replacements were made. The structural dynamics also revealed that hydrogen bonds were strongly coupled to each other; the loss of one hydrogen-bond interaction had a profound effect on the entire hydrogen-bonding network. The A(q) binding data revealed that an ethylene isostere glycopeptide unexpectedly bound more strongly to A(q) than the corresponding (E)-alkene, which is in contrast to the trend observed for the other isosteres. Analysis of the MD trajectories revealed that the complex conformation of this ethylene isostere was structurally different and had an altered molecular interaction pattern compared to the other A(q)/glycopeptide complexes. The introduced amide-bond isosteres also affected the interactions of the glycopeptide/A(q) complexes with T-cell receptors. The dynamic variation of the patterns and strengths of the hydrogen-bond interactions in the class II MHC system is of critical importance for the class II MHC/peptide/TCR signaling system.

  • 318.
    Andersson, Jana
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    En studie av gruvindustrins påverkan på ett akvatiskt system.: Brubäckens påverkan på Granforsmagasinet2005Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
  • 319.
    Andersson, Jannika
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    How does nutrients and light affect algal growth in Swedish headwater streams?: A study using nutrient diffusing substrate and natural gradients of light2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Gaining knowledge about what factors determine benthic algal biomass and productivity is vital for understanding food webs in aquatic systems, especially in woodland streams with naturally low rates of primary productivity. The aim of this study was to investigate what factors determine algal growth in Swedish headwater streams. Nutrients, in terms of nitrogen (N) and phosphorus (P), and light are factors known to affect algal growth. By using nutrient diffusing substrate (NDS) and different gradients of light, it was possible to test the importance of these factors. To determine the effect of the experiment, the study was carried out in a forested reference stream, which is largely shaded with extreme low nutrient levels, and in a stream running through a clear-cutting plantation with high nutrient levels and incident light. In the forested reference stream it became clear that algal growth increased by experimentally adding N (P<0.005), although light did not affect the productivity. In the stream running through the clear-cut, algal productivity increased significantly with higher levels of light (P<0.005), regardless of nutrient addition. The results from this study suggest that light only becomes the depending factor when sufficient amounts of nutrients are available. However, it is still unclear at what nutrient levels this shift occur, and therefore future research is recommended.

  • 320.
    Andersson, Jenny
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Dissecting the photosystem II light-harvesting antenna2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In photosynthesis, sunlight is converted into chemical energy that is stored mainly as carbohydrates and supplies basically all life on Earth with energy.

    In order to efficiently absorb the light energy, plants have developed the outer light harvesting antenna, which is composed of ten different protein subunits (LHC) that bind chlorophyll a and b as well as different carotenoids. In addition to the light harvesting function, the antenna has the capacity to dissipate excess energy as heat (feedback de-excitation or qE), which is crucial to avoid oxidative damage under conditions of high excitation pressure. Another regulatory function in the antenna is the state transitions in which the distribution of the trimeric LHC II between photosystem I (PS I) and II is controlled. The same ten antenna proteins are conserved in all higher plants and based on evolutionary arguments this has led to the suggestion that each protein has a specific function.

    I have investigated the functions of individual antenna proteins of PS II (Lhcb proteins) by antisense inhibition in the model plant Arabidopsis thaliana. Four antisense lines were obtained, in which the target proteins were reduced, in some cases beyond detection level, in other cases small amounts remained.

    The results show that CP29 has a unique function as organising the antenna. CP26 can form trimers that substitute for Lhcb1 and Lhcb2 in the antenna structure, but the trimers that accumulate as a response to the lack of Lhcb1 and Lhcb2 cannot take over the LHC II function in state transitions. It has been argued that LHC II is essential for grana stacking, but antisense plants without Lhcb1 and Lhcb2 do form grana. Furthermore, LHC II is necessary to maintain growth rates in very low light.

    Numerous biochemical evidences have suggested that CP29 and/or CP26 were crucial for feedback de-excitation. Analysis of two antisense lines each lacking one of these proteins clearly shows that there is no direct involvement of either CP29 or CP26 in this process. Investigation of the other antisense lines shows that no Lhcb protein is indispensable for qE. A model for feedback de-excitation is presented in which PsbS plays a major role.

    The positions of the minor antenna proteins in the PS II supercomplex were established by comparisons of transmission electron micrographs of supercomplexes from the wild type and antisense plants.

    A fitness experiment was conducted where the antisense plants were grown in the field and seed production was used to estimate the fitness of the different genotypes. Based on the results from this experiment it is concluded that each Lhcb protein is important, because all antisense lines show reduced fitness in the field.

  • 321.
    Andersson, Jens
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Potentiell etablering av strandvegetation längs torrfåror: En pilotstudie av en modelleringsmodell för miljöanpassade flöden2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Running water is an ecosystem that has high biodiversity despite its relatively small presence on the planet in terms of area. Water is also one of the most affected ecosystems, where hydropower is one of the actors with great impact and widespread use. Hydropower production often change the flow regime in rivers and damages, among other things, the littoral zone which is dependent on a natural flow regime. Without the natural flow regime's disturbance, the natural flora of the littoral zone is either displaced by upland vegetation, or it the zone becomes barren. One way to mitigate the negative effects of hydropower on the ecosystem are realesing water with a natural-like temporal variation in the original reaches. Reaches are often completely dry when water is redirected in to pass the turbines in the hydropower station. Previously there have been no attempts in Sweden to model the riparian potential below the dams using a theoretical environmental flow regime. This paper shows a way to inventory the potential for vegetation establishment of the riparian zone by field inventory of suitable substrate for riparian vegetation. For the inventoried locations, models of environmental flow at four levels of discharge (5, 10, 15 and 20% of the mean annual discharge) are used to predict the potetial extent of riparian vegetation. The modeling is done in ArcGIS using the "Riparian Topoghraphy Tool." The modelling show how much of the potential of water that inundates the riparian zone at varying levels of the hydropower production loss.

  • 322.
    Andersson, Jens
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Johansson, Frank
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Söderlund, Tony
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Interactions between predator- and diet-induced phenotypic changes in body shape of crucian carp2006In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 273, no 1585, p. 431-437Article in journal (Refereed)
    Abstract [en]

    Predator cues and diet, when studied separately, have been shown to affect body shape of organisms. Previous studies show that the morphological responses to predator absence/presence and diet may be similar, and hence could confound the interpretation of the causes of morphological differences found between groups of individuals. In this study, we simultaneously examined the effect of these two factors on body shape and performance in crucian carp in a laboratory experiment. Crucian carp (Carassius carassius) developed a shallow body shape when feeding on zooplankton prey and a deep body shape when feeding on benthic chironomids. In addition, the presence of chemical cues from a pike predator affected body shape, where a shallow body shape was developed in the absence of pike and a deep body shape was developed in the presence of pike. Foraging activity was low in the presence of pike cues and when chironomids were given as prey. Our results thereby suggest that the change in body shape could be indirectly mediated through differences in foraging activity. Finally, the induced body shape changes affected the foraging efficiency, where crucians raised on a zooplankton diet or in the absence of pike cues had a higher foraging success on zooplankton compared to crucian raised on a chironomid diet or in the presence of pike. These results suggest that body changes in response to predators can be associated with a cost, in terms of competition for resources.

  • 323. Andersson, Jon
    et al.
    Dynesius, Mats
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Hjalten, Joakim
    Short-term response to stump harvesting by the ground flora in boreal clearcuts2017In: Scandinavian Journal of Forest Research, ISSN 0282-7581, E-ISSN 1651-1891, Vol. 32, no 3, p. 239-245Article in journal (Refereed)
    Abstract [en]

    We studied short-term ground vegetation responses to stump harvesting by recording the occurrence of all species of bryophytes, vascular plants and the cover of soil disturbance on 20 clearcuts in the Southern and Middle Boreal zone in northern Scandinavia. All 20 clearcuts were slash-harvested and scarified and 10 of the clearcuts were also stump-harvested. The added effect of stump harvesting was assessed by comparing stump-harvested clearcuts with non-stump-harvested clearcuts. We tested whether stump harvesting causes extra soil disturbance compared to conventional forestry and if stump harvesting is affecting the assemblage, species richness and occurrence of individual species of vascular plants and bryophytes in boreal clearcuts. Our results revealed that stump harvesting causes an increase in the area of disturbed soil surface compared to conventional harvesting. Four of the most commonly occurring plant species in this area were significantly affected by stump harvesting, and Vaccinium vitis-idaea had a median occurrence of only 20% of that in non-stump-harvested clearcuts. The large impact on some plant species from a relatively modest increase of soil disturbance caused by stump harvesting suggest that stumps, with their slightly elevated bases, contributes to the survival of certain species on clearcuts.

  • 324.
    Andersson, Jon
    et al.
    Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
    Hjältén, Joakim
    Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
    Dynesius, Mats
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Long-term effects of stump harvesting and landscape composition on beetle assemblages in the hemiboreal forest of Sweden.2012In: Forest Ecology and Management, ISSN 0378-1127, E-ISSN 1872-7042, Vol. 271, p. 75-80Article in journal (Refereed)
    Abstract [en]

    Studies on the effects of stump harvesting on forest biodiversity are scarce and studies on long-term effects are until now non-existent. We evaluated such long-term effects by sampling beetles at 14 clear-cuts with and 14 clear-cuts without stump harvesting; harvesting had been done 21–28 years before this study. By using window traps, we collected 6429 individuals belonging to 432 species in 55 taxonomic families. To control for potentially confounding effects of among-site variations in landscape setting we also assessed forest age and volume of deciduous trees within the forest surrounding each site. The long-term effects from harvesting on beetle abundance, species richness and species composition was generally small in comparison to the influence of the characteristics of the surrounding forests. The species richness of the beetle family Latridiidae and the functional group fungivores appeared, however, to be negatively affected by the previous stump harvesting, while several other groups showed strong associations to the characteristics of the surrounding forest. We found little support for considerable long-term effects of stump harvesting on beetles flying in the stands. Long-term effects of stump harvesting at the landscape scale accumulated from harvest of many localities may still be severe, and should be the subject of future studies.

  • 325. Andersson, Jon
    et al.
    Hjältén, Joakim
    Dynesius, Mats
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wood-Inhabiting Beetles in Low Stumps, High Stumps and Logs on Boreal Clear-Cuts: Implications for Dead Wood Management2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 3, article id e0118896Article in journal (Refereed)
    Abstract [en]

    The increasing demand for biofuels from logging residues require serious attention on the importance of dead wood substrates on clear-cuts for the many forestry-intolerant saproxylic (wood-inhabiting) species. In particular, the emerging harvest of low stumps motivates further study of these substrates. On ten clear-cuts we compared the species richness, abundance and species composition of saproxylic beetles hatching from four to nine year old low stumps, high stumps and logs of Norway spruce. By using emergence traps we collected a total of 2,670 saproxylic beetles among 195 species during the summers of 2006, 2007 and 2009. We found that the species assemblages differed significantly between high stumps and logs all three years. The species assemblages of low stumps, on the other hand, were intermediate to those found in logs and high stumps. There were also significant difference in species richness between the three examined years, and we found significant effect of substrate type on richness of predators and fungivores. As shown in previous studies of low stumps on clear-cuts they can sustain large numbers of different saproxylic beetles, including red-listed species. Our study does, in addition to this fact, highlight a possible problem in creating just one type of substrate as a tool for conservation in forestry. Species assemblages in high stumps did not differ significantly from those found in low stumps. Instead logs, which constitute a scarcer substrate type on clear-cuts, provided habitat for a more distinct assemblage of saproxylic species than high stumps. It can therefore be questioned whether high stumps are an optimal tool for nature conservation in clear-cutting forestry. Our results also indicate that low stumps constitute an equally important substrate as high stumps and logs, and we therefore suggest that stump harvesting is done after carefully evaluating measures to provide habitat for saproxylic organisms.

  • 326.
    Andersson, Jonas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Ion recombination in liquid ionization chambers: development of an experimental method to quantify general recombination2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    An experimental method (the two-dose-rate method) for the correction of general recombination losses in liquid ionization chambers has been developed and employed in experiments with different liquids and radiation qualities. The method is based on a disassociation of initial and general recombination, since an ionized liquid is simultaneously affected by both of these processes.

    The two-dose-rate method has been compared to an existing method for general recombination correction for liquid ionization chambers, and has been found to be the most robust method presently available.

    The soundness of modelling general recombination in liquids on existing theory for gases has been evaluated, and experiments indicate that the process of general recombination is similar in a gas and a liquid. It is thus reasonable to employ theory for gases in the two-dose-rate method to achieve experimental corrections for general recombination in liquids. There are uncertainties in the disassociation of initial and general recombination in the two-dose-rate method for low applied voltages, where initial recombination has been found to cause deviating results for different liquids and radiation qualities.

    Sensitivity to ambient electric fields has been identified in the microLion liquid ionization chamber (PTW, Germany). Experimental data may thus be perturbed if measurements are conducted in the presence of ambient electric fields, and the sensitivity has been found to increase with an increase in the applied voltage. This can prove to be experimentally limiting since general recombination may be too severe for accurate corrections if the applied voltage is low.

  • 327.
    Andersson, Jonas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Radiation Dosimetry for CBCT – Quality Control and Applied Dosimetry2015Conference paper (Refereed)
    Abstract [en]

    The use of Cone Beam CT (CBCT) devices in health care has increased in recent years. Unfortunately, this trend has not been followed by a standardization of dose metrics for Quality Control (QC), or a necessary evolution of applied dosimetry for assessment of patient dose.

    The European Federation of Organisations in Medical Physics (EFOMP) has drafted a report on the property of QC for CBCT devices. The report contains objective, practical and unifying methodology for QC of CBCT used in oral radiology, radiotherapy, interventional radiology and guided surgery. The dose metrics discussed include the Computed Tomography Dose Index (CTDI), Kerma-Area Product (KAP) and detector incident air kerma. The report concludes that KAP-meters are preferable for QC as long as they can be mounted on the X-ray tube housing. Otherwise measurements of detector incident kerma seem to offer a practical solution for QC.

    The European Radiation Dosimetry Group (EURADOS) are preparing a literature review on patient dose from various applications of CBCT, which will in part be included in the EFOMP report. Most studies on patient dose from CBCT examinations and interventional procedures are based on thermoluminescent dosimeter (TLD) measurements in Rando phantoms. While helpful to the community, these studies yield substantial uncertainty when applied in the clinical reality of medical physicists working with justification and optimization. Applied dosimetry for CBCT needs to evolve and adopt recent theoretical advances to allow robust estimates of patient dose.

  • 328.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Granberg, Christoffer
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Riklund, Katrine
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology.
    A novel system for quality assurance of radiology equipment2018In: Eurosafe Imaging 2018, 2018Conference paper (Refereed)
  • 329.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Johansson, Erik
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Tölli, Heikki
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    On the property of measurements with the PTW microLion chamber in continuous beam2012In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 39, no 8, p. 4775-4787Article in journal (Refereed)
    Abstract [en]

    Purpose: The performance of liquid ionization chambers, which may prove to be useful tools in the field of radiation dosimetry, is based on several chamber and liquid specific characteristics. The present work investigates the performance of the PTW microLion liquid ionization chamber with respect to recombination losses and perturbations from ambient electric fields at various dose rates in continuous beams.

    Methods: In the investigation, experiments were performed using two microLion chambers, containing isooctane (C8H18) and tetramethylsilane (Si(CH3)4) as the sensitive media, and a NACP-02 monitor chamber. An initial activity of approximately 250 GBq 18F was employed as the radiation source in the experiments. The initial dose rate in each measurement series was estimated to 1.0 Gy min-1 by Monte Carlo simulations and the measurements were carried out during the decay of the radioactive source. In the investigation of general recombination losses, employing the two-dose-rate method for continuous beams, the liquid ionization chambers were operated at polarizing voltages 25, 50, 100, 150, 200 and 300 V. Furthermore, measurements were also performed at 500 V polarizing voltage in the investigation of the sensitivity of the microLion chamber to ambient electric fields.

    Results: The measurement results from the liquid ionization chambers, corrected for general recombination losses according to the two-dose-rate method for continuous beams, had a good agreement with the signal to dose linearity from the NACP-02 monitor chamber for general collection efficiencies above 70%. The results also displayed an agreement with the theoretical collection efficiencies according to the Greening theory, except for the liquid ionization chamber containing isooctane operated at 25 V. At lower dose rates, perturbations from ambient electric fields were found in the microLion chamber measurement results. Due to the perturbations, measurement results below an estimated dose rate of 0.2 Gy min-1 were excluded from the present investigation of the general collection efficiency. The perturbations were found to be more pronounced when the chamber polarizing voltage was increased.

    Conclusions: By using the two-dose-rate method for continuous beams, comparable corrected ionization currents from experiments in low- and medium energy photon beams can be achieved. However, the valid range of general collection efficiencies has been found to vary in a comparison between experiments performed in continuous beams of 120 kVp x-ray, and the present investigation of 511 keV annihilation photons. At very high dose rates in continuous beams, there are presently no methods that can be used to correct for general recombination losses and at low dose rates the microLion chamber may be perturbed by ambient electric fields. Increasing the chamber polarizing voltage, which diminishes the general recombination effect, was found to increase the microLion chamber sensitivity to ambient electric fields. Prudence is thus advised when employing the microLion chamber in radiation dosimetry, as ambient electric fields of the strength observed in the present work may be found in many common situations. Due to uncertainties in the theoretical basis for recombination losses in liquids, further studies on the underlying theories for the initial and general recombination effect are needed if liquid ionization chambers are to become a viable option in high precision radiation dosimetry.

  • 330.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Kaiser, Franz-Joachim
    Gómez, Faustino
    Jäkel, Oliver
    Pardo-Montero, Juan
    Tölli, Heikki
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    A comparison of different experimental methods for general recombination correction for liquid ionization chambers2012In: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560, Vol. 57, no 21, p. 7161-7175Article in journal (Refereed)
    Abstract [en]

    Radiation dosimetry of highly modulated dose distributions requires a detector with a high spatial resolution. Liquid filled ionization chambers (LICs) have the potential to become a valuable tool for the characterization of such radiation fields. However, the effect of an increased recombination of the charge carriers, as compared to using air as the sensitive medium has to be corrected for. Due to the presence of initial recombination in LICs, the correction for general recombination losses is more complicated than for air-filled ionization chambers. In the present work, recently published experimental methods for general recombination correction for LICs are compared and investigated for both pulsed and continuous beams. The experimental methods are all based on one of two approaches, either measurements at two different dose rates (two-dose-rate methods), or measurements at three different LIC polarizing voltages (three-voltage methods). In a comparison with the two-dose-rate methods, the three-voltage methods fail to achieve accurate corrections in several instances, predominantly at low polarizing voltages and dose rates. However, for continuous beams in the range of polarizing voltages recommended by the manufacturer of the LICs used, the agreement between the different methods is generally within the experimental uncertainties. For pulsed beams, the agreement between the methods is poor. The inaccuracies found in the results from the three-voltage methods are associated with numerical difficulties in solving the resulting equation systems, which also make these methods sensitive to small variations in the experimental data. These issues are more pronounced for the case of pulsed beams. Furthermore, the results suggest that the theoretical modelling of initial recombination used in the three-voltage methods may be a contributing factor to the deviating results observed.

  • 331.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Pavlicek, William
    Patient organ dose with computed tomography - a review of present methodology and DICOM information: executive summary of the joint report of AAPM task group 246 and EFOMP2016In: ECR 2016 Book of Abstracts, 2016, Vol. 7, no 1, article id B0303Conference paper (Refereed)
    Abstract [en]

    Purpose: The justification and optimisation of medical imaging employing ionizing radiation have been intensely discussed in recent years, particularly for computed tomography (CT). A key point in this discussion is the estimation of patient dose, which commonly employs radiation output metrics developed for quality assurance and no patient specific information. Such patient dose estimates are of limited value, and more refined methods needs to be promoted and provided to the community.

    Methods and Materials: AAPM Task Group 246 was formed in 2013, and in a joint venture with EFOMP charged with summarizing present methodology and DICOM information available for estimating patient dose with computed tomography.

    Results: The Joint Report of AAPM Task Group 246 and EFOMP is a comprehensive resource for the clinical medical physicist. The possibilities of patient specific dosimetry from the Computed Tomography Dose Index (CTDIvol), to the Size-Specific Dose Estimates (SSDE) and advanced Monte Carlo methods are discussed together with available DICOM information, as well as practical examples on how patient dose estimates can be achieved. The report also summarizes important factors contributing to the uncertainty in patient dose estimates and gives examples of achievable confidence intervals.

    Conclusion: The SSDE and Monte Carlo methods can together with detailed scanner, examination and patient specific DICOM information offer refined estimates of patient dose for justification and optimisation of CT examinations. Given the present robustness of available methods AAPM Task Group 246 and EFOMP recommend that all reports of patient dose should be accompanied by estimates of the associated uncertainty.

  • 332.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Tölli, Heikki
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Modeling ion recombination in liquid ionization chambers: Improvement and analysis of the two-dose-rate method2017In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 44, no 11, p. 5977-5987Article in journal (Refereed)
    Abstract [en]

    Purpose: The use of liquid ionization chambers can provide useful information to endeavors with radiation dosimetry for highly modulated beams. Liquid ionization chambers may be particularly suitable for computed tomography applications where conventional ionization chambers do not present a high enough sensitivity for the spatial resolution required to characterize common X-ray beams. Due to the sensitivity, which leads to high charge densities, liquid ionization chambers can suffer from large recombination losses leading to degradation in signal to dose rate linearity. To solve this problem, a two-dose-rate method for general recombination correction has been proposed for liquid ionization chambers. However, the valid range of recombination losses that the method can accurately account for has been found to vary depending on radiation quality. The present work provides an in-depth analysis of the performance of the two-dose-rate method. Furthermore, the soundness of applying gas theory to liquids is investigated by using the two-dose-rate method.

    Methods: In the present work, the two-dose-rate method for general recombination correction of liquid ionization chambers used in continuous beams is studied by employing theory for gas-filled ionization chambers. An approximate relation for the general collection efficiency containing a material-specific parameter that is traceable to liquids has been derived for theoretical and experimental investigation alongside existing theory. Furthermore, the disassociation between initial and general recombination in the method is analyzed both theoretically and experimentally.

    Results: The results indicate that liquids and gases share general recombination characteristics, where the liquids investigated (isooctane and tetramethylsilane) to a large extent mimic the behavior theoretically expected in gases. Furthermore, it is shown that the disassociation between initial and general recombination in the two-dose-rate method is an approximation that depends on the relation between initial recombination and the collecting electric field strength at the dose rates used.

    Conclusions: Due to the approximation used to separate initial and general recombination the valid range of collection efficiencies for the two-dose-rate method will not only depend on the model used to describe general recombination but also on the type of liquid and radiation beam quality. As there is no robust theory for initial recombination in liquids to apply, the valid range of general collection efficiencies for the two-dose-rate method should be experimentally evaluated for each radiation dosimetry application.

  • 333.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Tölli, Heikki
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    The Use of Liquid Ionization Chambers in Radiation Dosimetry2012In: World Congress on Medical Physics and Biomedical Engineering May 26-31, 2012 Beijing, China / [ed] Mian Long, Springer, 2012Conference paper (Refereed)
    Abstract [en]

    Liquid ionization chambers (LICs) have found applications in many fields in radiation dosimetry, e.g. IMRT, hadron therapy, brachytherapy and computed tomography. The wide range of applications is made possible due to the high sensitivity of LICs, allowing them to be manufactured with small physical dimensions of the chamber body and the effective measurement volume. Furthermore, the commonly used liquids (such as isooctane) have radiation absorption characteristics similar to water, introducing only small fluence perturbation effects as compared to conventional dosimeters. The small dimension of the effective measurement volume is beneficial for the quantification of radiation beams with steep gradients, while retaining a high measurement signal with good statistical properties. However, the interpretation of measurement results is not straight-forward due to several factors influencing their performance. Here, the main problems are recombination effects and particle type- and energy dependence, which may cause severe non-linear effects. The loss of measurement signal in LICs is due to both initial and general recombination. In the present work it is shown that the general recombination effect can be treated with in a similar manner as for air-filled ionization chambers, while there are currently no theories that adequately describe the initial recombination effect for LICs. Furthermore, the relationship between energy dependence and recombination losses in LICs are evaluated at different radiation qualities. Recently developed methods for the correction of general recombination losses in LICs are discussed and their validity evaluated.

  • 334.
    Andersson, Karin
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Prefibrillar oligomeric Transthyretin mutants - amyloid conformation, toxicity and association with Serum amyloid P component2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Amyloidoses represent a heterogeneous group of diseases characterized by abnormal protein metabolism leading to extracellular deposition of fibrillar, proteinaceous amyloid in various tissues and organs of the body. To date more than 20 different proteins have been linked to diseases with amyloid depositions, of which Alzheimer’s disease and the prion-associated diseases are the most well known. Despite the origin of protein in the amyloid, the fibrils share some common biochemical and biophysical properties such as a diameter of 8-13 nm, a β-pleated sheet secondary structure packed in an ordered crystal-like way, Congo red and thioflavin binding with characteristic spectroscopic patterns and decoration of the fibrils with Serum amyloid P component and glycoseaminoglycans.

    The plasma protein transthyretin (TTR) is associated with familial amyloidosis with polyneuropathy (FAP) and senile systemic amyloidosis (SSA). FAP is a lethal, autosomal inherited disorder caused by point mutations in the TTR-gene. More than 80 different mutations have been associated with amyloid formation and linked to FAP. The interpretation is that amino acid replacements at different sites of the polypeptide lead to reduced stability. Mutant TTR were constructed that have a strong tendency to self-aggregate under physiological conditions. The precipitates were shown to be amyloid by staining with thioflavin T and Congo red. As the mutants were sensitive to trypsin cleavage compared to plasma TTR, we suggest that the mutants represent amyloid precursors or that they may share structural properties with intermediates on a pathway leading to amyloid deposition. Monoclonal antibodies were generated that exclusively recognize the amyloidogenic folding of TTR providing direct biochemical evidence for a structural change in amyloidogenic intermediates. Two cryptic epitopes were mapped to a domain of TTR, where most mutations associated with amyloidosis occur and is proposed to be displaced at the initial phase of amyloid formation. Amyloidogenic intermediates of TTR were shown to induce a toxic, free radical dependent, response in cultured neuroblastoma cells. Morphological studies revealed a correlation between toxicity (apoptosis) and the presence of immature amyloid suggesting that mature full-length fibrils represent an inert end stage, which might serve as a rescue mechanism.

    Serum amyloid P component (SAP) is a highly conserved plasma glycoprotein universally found associated with amyloid depositions independently of protein origin. SAP’s role in amyloid formation is contradictory since both inhibition and promotion of aggregation have been shown in the case of fibril formation from the Aβ peptide of Alzheimer’s disease. Amyloidogenic prefibrils of TTR were shown to bind SAP and no interference with aggregation was detected. SAP co-localize in patches with mutant TTR on the surface of neuroblastoma cells and prevent apoptosis induced by mutant TTR and Aβ peptide, while several other molecules known to decorate amyloid fibrils were without effect.

  • 335.
    Andersson, Karin
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Olofsson, Anders
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Holm Nielsen, Ellen
    Svehag, SvenErik
    Lundgren, Erik
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Only amyloidogenic inermediates of transthyretin induce apoptosis2002In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 294, no 2, p. 309-314Article in journal (Refereed)
    Abstract [en]

    In diseases like Alzheimer's disease and familial amyloidotic polyneuropathy (FAP) amyloid deposits co-localize with areas of neurodegeneration. FAP is associated with mutations of the plasma protein transthyretin (TTR). We can here show an apoptotic effect of amyloidogenic mutants of TTR on a human neuroblastoma cell line. Toxicity could be blocked by catalase indicating a free oxygen radical dependent mechanism. The toxic effect was dependent on the state of aggregation and unexpectedly mature fibrils from FAP-patients who failed to exert an apoptotic response. Morphological studies revealed a correlation between toxicity and the presence of immature amyloid. Thus, we can show that toxicity is associated with early stages of fibril formation and propose that mature full-length fibrils represent an inert end stage, which might serve as a rescue mechanism. 

  • 336.
    Andersson, Kennet
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Effects of Physiological Variations2006Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Heart ischemia, the precursor to an infarction, is one of the most common diseases in the western world. Today, the electrocardiogram or ECG is the most widely used tool to diagnose the disease. However, it often fails to detect the ischemia or to give an adequate picture of the size and location.

    Therefore, the potential of increasing knowledge obtained through mathe- matical models is very high. In this thesis the bidomain model is used to describe the electrical activity in the heart and body with ischemia incorporated into the model. To solve the equations set up by the bidomain model, the finite element method is used. Different physiological variations have been made to the body, these include changing the location of the heart and varying the conductivities in the body. The solution to the equations is then studied at the body surface. The main question asked is whether it is possible to detect the location and size of different types of ischemia by analyzing the solution.

    The methods used for this have been Singular Value Decomposition and Su- pervised learning. The different vectors obtained from the decomposition are used to distinguish the location and size of the ischemia for different physiolog- ical variations.

    The results show that it is possible to distinguish the location of the ischemia but that it probably will be more difficult to find the correct size since the change in size is harder to separate from other physiological variations, such as the conductivity of the body.

    Although relatively simple methods have been used, they indicate that, with further development, they can be used for the purpose of detecting the different ischemia. 

  • 337.
    Andersson, Kristoffer
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Selective detection of TNT withmodified SERS-surfaces: Investigation of TNT adsorption and detection using goldand silver nano structured surfaces modified by cysteineand cysteamine2010Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In the search for trace amounts of explosives in various environmental samples, the

    analytical procedure is in need of improvements. If it is for national security or for

    environmental purposes the detection of trace amounts of for example 2,4,6-

    trinitrotoluene (TNT) is a costly and time consuming procedure. The use of Raman

    spectrometry for trace amounts detection is one of the research areas that are in the

    advancement and mainly because of the discovery of Surface-Enhanced Raman

    spectroscopy (SERS). Raman spectrometry detects the inelastically scattered light

    from molecules giving a fingerprint spectrum that can be interpreted and species can

    be detected. The inelastically scattering of light only occurs in a small amount of the

    molecules making the signal low and sensitive for interferences. SERS enhances the

    signal from the molecules making it possible to detect very low concentrations. The

    surfaces used in SERS need to be selective for the wanted species to be useful for the

    analysis of environmental samples that often contains a wide variety of compounds.

    This project’s aim was to investigate the possibility of modifying gold- and silvercoated

    SERS surfaces (provided by DTU Nanotech) to get a selective detection of

    trace amounts of TNT in water and air samples.

    The results from the modification indicated some problems with the surfaces. The

    modification molecules were cysteine or cysteamine. The hypothesis was that both of

    them should bind to the surface by sulphur bond. But for cysteine this was not the

    case. The results indicated a binding of the carboxyl group making the use of the

    modification for the selective detection of TNT impossible. The modification by

    cysteamine was more successful but the detection of TNT in water samples was hard

    to get clear results from. The detection of TNT in air samples was carried out by a

    method never tested before using a so-called Linkam cell in conjunction with a TNT

    treated GC-column which together create a controlled environment. The results from

    this experiment were very positive where a clear SERS-signal from TNT could be

    detected.

  • 338.
    Andersson Lundberg, Malin
    Umeå University, Faculty of Science and Technology, Department of Science and Mathematics Education.
    Hur finner vi elever i behov av särskilt stöd i matematik i årskurs 1-3?2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    En betydelsefull faktor för att kunna förebygga eller minska elevers svårigheter i matematik är att de upptäcks tidigt. Det är viktigt att ha kunskap om vilka signaler som ska betraktas som avvikande och kräver en särskild utredning (Butterworth, 2011; Malmer, 2006).

    Syftet med denna rapport är att undersöka och analysera lärares,speciallärares och specialpedagogers strategier att identifiera SUM-elever, årskurs 1-3 via deras beskrivningar. Studien har en kvalitativ ansats med vissa kvantitativa delar. Metoderna har varit dels semistrukturerade intervjuer med specialpedagoger och speciallärare och dels enkäter med många öppna frågor till lärarna.

    Undersökningen visar bland annat att pedagogerna ofta använder sig av olika kartläggningsmaterial för att upptäcka SUM-elever. De upptäcker även SUM-eleverna i det dagliga arbetet och i olika former av dialoger med andra pedagoger, elever och vårdnadshavare. Kartläggningsmaterial används olika, på vissa skolor genomförs kartläggning regelbundet efter en viss plan och på andra skolor används kartläggning vid behov. Vidare varierar det hur specialpedagogen och specialläraren använder sin tid för att hitta SUM-elever. Vissa bedömer det som betydelsefullt att observera och vara i klassen, andra bedömer det som mer verkningsfullt att handleda personal och jobba enskilt med elever för att upptäcka elever i behov av särskilt stöd i matematik.

    I undersökningen framkom att pedagogerna inte är konsekventa i sina åsikter när det gäller hur de är grundade de specialpedagogiska perspektiven. De olika tankar som pedagogerna ger uttryck för kan sägas spegla hela skalan av specialpedagogiska perspektiv.

    Avslutningsvis kan man säga att pedagogerna anser att lärarnas behörighet och kompetens är det mest avgörande för om SUM-eleverna ska upptäckas. Även klasstorleken har viss betydelse för möjligheter att upptäcka SUM-elever. Speciallärarna och specialpedagogerna anser utöver detta att ett bra kartläggningsmaterial och att erfarenhet har betydelse då det gäller att upptäcka SUM-elever. Det framkom även att pedagogerna tyckte att det saknades tydlig ledning och engagemang från rektor i arbetet att upptäcka SUM-elever.

    Nyckelord: dialog, kartläggning, specialpedagogiska perspektiv, SUM-elev, särskilt undervisningsbehov i matematik.

     

  • 339.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Physics.
    Construction of force measuring optical tweezers instrumentation and investigations of biophysical properties of bacterial adhesion organelles2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Optical tweezers are a technique in which microscopic-sized particles, including living cells and bacteria, can be non-intrusively trapped with high accuracy solely using focused light. The technique has therefore become a powerful tool in the field of biophysics. Optical tweezers thereby provide outstanding manipulation possibilities of cells as well as semi-transparent materials, both non-invasively and non-destructively, in biological systems. In addition, optical tweezers can measure minute forces (< 10-12 N), probe molecular interactions and their energy landscapes, and apply both static and dynamic forces in biological systems in a controlled manner. The assessment of intermolecular forces with force measuring optical tweezers, and thereby the biomechanical structure of biological objects, has therefore considerably facilitated our understanding of interactions and structures of biological systems.

    Adhesive bacterial organelles, so called pili, mediate adhesion to host cells and are therefore crucial for the initial bacterial-cell contact. Thus, they serve as an important virulence factor. The investigation of pili, both their biogenesis and their expected in vivo properties, brings information that can be of importance for the design of new drugs to prevent bacterial infections, which is crucial in the era of increased bacterial resistance towards antibiotics.

    In this thesis, an experimental setup of a force measuring optical tweezers system and the results of a number of biomechanical investigations of adhesive bacterial organelles are presented. Force measuring optical tweezers have been used to characterize three different types of adhesive organelles under various conditions, P, type 1, and S pili, which all are expressed by uropathogenic Escherichia coli. A quantitative biophysical force-extension model, built upon the structure and force response, has been developed. It is found, that this model describes the biomechanical properties for all three pili in an excellent way. Various parameters in their energy landscape, e.g., bond lengths and transition barrier heights, are assessed and the difference in behavior is compared. The work has resulted in a method that in a swift way allows us to probe different types of pili with high force and high spatial resolution, which has provided an enhanced understanding of the biomechanical function of these pili.

  • 340.
    Andersson, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Björnham, Oscar
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Bullitt, Esther
    Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St., Boston MA, USA.
    Svantesson, Mats
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Uhlin, Bernt Eric
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Differentiating pili expressed by enterotoxigenic and uropathogenic escherichia coli with optical tweezersManuscript (preprint) (Other academic)
    Abstract [en]

    Enterotoxigenic Escherichia coli (ETEC) attach to the host epithelium in the intestinal tract via specific adhesion organelles expressed on the cell membrane. We investigate, by force measuring optical tweezers, the intrinsic biomechanical properties and kinetics of the colonization factor I (CFA/I) at a single pilus level. The measurements indicate that CFA/I pili are helix-like structures that can both be unraveled to a linearized polymer by applying a small external force, 7.5 ± 1.5 pN but also regain its helix-like structure when the applied force is reduced. The data confirm that layer-to-layer interactions, that stabilize the helix-like structure, are much weaker than the interactions found in pili expressed by Uropathogenic Escherichia coli (UPEC). It is also found, contrary to previous results assessed from UPEC pili, that the CFA/I undergo in some cases a sudden structural change, a force drop of ~2 pN, when unraveled from the helix-like configuration to an open helical linearized fiber. These data suggest a rotation of the filament about its helical axis, followed by a region in which the force required to extend the pili further increases rapidly. During this final elongation to a super-extended fiber, CFA/I pili do not show any structural transition as seen for UPEC pili. In addition, the CFA/I pili show faster kinetics than UPEC pili that allows for a larger dynamic regime of in vivo shear forces. The unfolding and refolding possibility points toward an organelle that has evolved to allow for dynamic damping of external forces and handling of harsh motion without breaking.

  • 341.
    Andersson, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Czerwinski, Fabian
    The Niels Bohr Institute, University of Copenhagen, Denmark.
    Oddershede, L B
    The Niels Bohr Institute, University of Copenhagen, Denmark.
    Optimizing active and passive calibration of optical tweezers2011In: Journal of optics, ISSN 0150-536X, Vol. 13, no 4Article in journal (Refereed)
    Abstract [en]

    To obtain quantitative information from optical trapping experiments it is essential to perform a precise force calibration. Therefore, sources of noise should be pinpointed and eliminated. Fourier analysis is routinely used to calibrate optical trapping assays because it is excellent for pinpointing high frequency noise. In addition, Allan variance analysis is particularly useful for quantifying low frequency noise and for predicting the optimal measurement time. We show how to use Allan variance in combination with Fourier analysis for optimal calibration and noise reduction in optical trapping assays. The methods are applied to passive assays, utilizing the thermal motion of a trapped particle, and to active assays where the bead is harmonically driven. The active method must be applied in assays where, for example, the viscoelastic properties of the medium or the size or shape of the trapped object are unknown. For measurement times shorter than the optimal calibration time the noise is larger in active than in the passive assays. For times equal to or longer than the optimal measurement time, though, the noise on passive and active assays is identical. As an example, we show how to quantify the influence on measurement noise of bead size and chamber geometry in active and passive assays.

  • 342.
    Andersson, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Fällman, Erik
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Uhlin, Bernt Eric
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Axner, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Force measuring optical tweezers system for long time measurements of P pili stability2006In: Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues IV / [ed] Farkas, DL, Nicolau, DV, Leif, RC, 2006, Vol. 6088, p. 608810-Conference paper (Refereed)
    Abstract [en]

    A force-measuring optical tweezers instrumentation and long time measurements of the elongation and retraction of bacterial fimbriae from Uropathogenic E. coli (UPEC) under strain are presented. The instrumentation is presented in some detail. Special emphasis is given to measures taken to reduce the influence of noise and drifts in the system and from the surrounding, which makes long term force measurements possible. Individual P pili from UPEC bacteria were used as a biological model system for repetitive unfolding and refolding cycles of bacterial fimbriae under equilibrium conditions. P pili have evolved into a three-dimensional helix-like structure, the PapA rod, that can be successively and significantly elongated and/or unfolded when exposed to external forces. The instrumentation is used for characterization of the force-vs.-elongation response of the PapA rod of individual P pili, with emphasis on the long time stability of the forced unfolding and refolding of the helical structure of the PapA rod. The results show that the PapA rod is capable of withstanding extensive strain, leading to a complete unfolding of the helical structure, repetitive times during the life cycle of a bacterium without any noticeable alteration of the mechanical properties of the P pili. This function is believed to be importance for UPEC bacteria in vivo since it provides a close contact to a host cell (which is an initial step of invasion) despite urine cleaning attempts.

  • 343.
    Andersson, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Svantesson, Mats
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Björnham, Oscar
    Swedish Defence Research Agency (FOI), SE-906 21 Umeå, Sweden.
    Badahdah, Arwa
    Department of Oral Biology, Boston University School of Dental Medicine.
    Uhlin, Bernt Eric
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Bullitt, Esther
    Department of Physiology and Biophysics, Boston University School of Medicine.
    A structural basis for sustained bacterial adhesion: Biomechanical properties of CFA/I Pili2012In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 415, no 5, p. 918-928Article in journal (Refereed)
    Abstract [en]

    Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrheal disease worldwide. Adhesion pili (or fimbriae), such as the CFA/I (colonization factor antigen I) organelles that enable ETEC to attach efficiently to the host intestinal tract epithelium, are critical virulence factors for initiation of infection. We characterized at single organelle level the intrinsic biomechanical properties and kinetics of individual CFA/I pili, demonstrating that weak external forces (7.5 pN) are sufficient to unwind the intact helical filament of this prototypical ETEC pilus and that it quickly regains its original structure when the force is removed. While the general relationship between exertion of force and an increase in the filament length for CFA/I pili associated with diarrheal disease is analogous to that of P-pili and type 1 pili, associated with urinary tract and other infections, the biomechanical properties of these different pili differ in key quantitative details. Unique features of CFA/I pili, including the significantly lower force required for unwinding, the higher extension speed at which the pili enter a dynamic range of unwinding, and the appearance of sudden force drops during unwinding can be attributed to morphological features of CFA/I pili including weak layer-to-layer interactions between subunits on adjacent turns of the helix, and the approximately horizontal orientation of pilin subunits with respect to the filament axis. Our results indicate that ETEC CFA/I pili are flexible organelles optimized to withstand harsh motion without breaking, resulting in continued attachment to the intestinal epithelium by the pathogenic bacteria that express these pili.

  • 344. Andersson, Magnus
    et al.
    Vincent, Jonathan
    Uppsala Univ, Dept Photochem & Mol Sci.
    van der Spoel, David
    Davidsson, Jan
    Neutze, Richard
    A Proposed Time-Resolved X-Ray Scattering Approach to Track Localand Global Conformational Changes in Membrane Transport Proteins2008In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 16, p. 21-28Article in journal (Refereed)
    Abstract [en]

    Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that underpin the alternating access paradigm for membrane transport proteins.

  • 345.
    Andersson, Maja
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Enhancing content discovery in Video on Demand services for children2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The media landscape is changing and Internet-based streaming services for children are becoming increasingly popular. The concept of online streaming extends freedom and control over content selection but discovering new content is often experienced as troublesome. The objective of this thesis is to identify parameters to make it easier for users of streaming services for children to discover and watch unfamiliar programs. Guidelines are formed based on literature studies, interviews, observations, a survey, a benchmark, data analysis with Adobe Analytics, a workshop and finally user tests with prototypes. These guidelines conclude that content should be categorized, dynamicized, highlighted and socially engaging. Categorization based on age is primarily important but interests and genres can also be used to make children more interested in a title. Content should be dynamic, customizable and personal to each user to give more accurate recommendations based on age and interests. Making one alternative more visually prominent will make this alternative more interesting especially for younger children and social features with information about other users opinions can motivate a decision to discover new content among older children. 

  • 346.
    Andersson, Marcus
    Umeå University, Faculty of Social Sciences, Department of Psychology.
    Complexity and problem solving: A tale of two systems2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The purpose of this thesis is to investigate if increasing complexity for a problem makes a difference for a learning system with dual parts. The dual parts of the learning system are modelled after the Actor and Critic parts from the Actor-Critic algorithm, using the reinforcement learning framework. The results conclude that not any difference can be found in the relative performance in the Actor and Critic parts when increasing the complexity of a problem. These results could depend on technical difficulties in comparing the environments and the algorithms. The difference in complexity would then be non-uniform in an unknowable way and uncertain to use as comparison. If on the other hand the change of complexity is uniform, this could point to the fact that there is an actual difference in how each of the actor and critic handles different types of complexity. Further studies with a controlled increase in complexity are needed to establish which of the scenarios is most likely to be true. In the discussion an idea is presented of using the Actor-Critic framework as a model to understand the success rate of psychological treatments better.

  • 347.
    Andersson, Marie
    Umeå University, Faculty of Medicine, Molecular Biology (Faculty of Medicine).
    Immunopathogenesis of relapsing fever borreliosis2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Relapsing fever (RF) is caused by different species of Borrelia transmitted by soft ticks or by the human body louse. Illness is characterized by reappearing peaks of high concentrations of spirochetes in blood, concordant with fever peaks separated by asymptomatic periods. Neuroborreliosis is one of the most severe manifestations of RF borreliosis. To understand the immune response during early RF, we analyzed immune cells in brain and kidney of mice infected with B. crocidurae during the acute infection. Our results indicate that brain defense is comprised primarily of innate immune cells. Despite the infiltration of innate immune cells, Borrelia was not completely eradicated. A failure of the host brain to clear the bacteria may give the pathogen a niche where it can persist. Using our mouse model, we revealed that Borrelia duttonii could persist in the mouse brain for up to 270 days, without being present in the circulation. The infection was silent with no change in host gene expression, and the spirochetes could re-enter the circulation after immunosuppression. We propose that the brain is used by the pathogen to evade host immunity and serves as a possible natural reservoir for B. duttonii, a spirochete that has rarely been found in any mammalian host other than man. Borrelia-induced complications during pregnancy have been reported, and are especially common in RF. In our established mouse model of gestational RF, we could show that the fetuses suffered from severe pathology and growth retardation, probably as a consequence of placental destruction. We could also show trans-placental transmission of the bacteria leading to neonatal RF. Surprisingly, pregnant dams had a lower bacterial load and less severe disease, showing that pregnancy has a protective effect during RF. We have used the gestational RF model to investigate host factors favoring disease resolution. Because the spleen is the primary organ responsible for trapping and removing blood-borne pathogens, we have compared temporal changes in spleen immune cell populations and cytokine/chemokine induction during the infection. Spleens of pregnant mice had earlier neutrophil infiltration, as well as faster and higher production of pro-inflammatory mediators. This rapid, robust response suggests a more effective host defense. Thus, an enhanced pro-inflammatory response during pregnancy imparts a distinct advantage in controlling the severity of relapsing fever infection.

  • 348.
    Andersson, Marléne
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Spillningsinventering av brunbjörn i väglöst land: Ett kompletterande arbetet till Länsstyrelsens björnspillningsinventering i Västerbotten år 20142014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The lack of information regarding the distribution of Ursus arctos arctos in the mountains of Västerbotten, Sweden, has led to many important questions about the occurrence of bears in these areas. Species distributions models, like MaxEnt, have shown to be a useful tool in species management. The objective of this study was therefore to determine if the distribution of bears in the southern part of the mountain range in Västerbotten could be predicted with MaxEnt. Data on the distribution of bear droppings were collected in the study area and used together with environmental variables. The resulting model had an AUC-value of 0,76, which is considered as good from a statistical point of view. Logistic regression over transect sampels in the study area was used to determine which variables that were most important to the species distribution. The regression gave no reliable results because the number of observations was too low. However, the method could yield valuable information if the sampel size is large enough. A field study to collect droppings from bears were made in Girifjället (where the probability of finding traces of bears was particulary high according to the MaxEnt analysis). No droppings were found in the area, but droppings were collected during the field study in an area with lower prediction value (but still relatively high). This leads to the conclusion that this method, with a few modifications, could be used together with logistics regression to get a better understanding of the distribution of bears in remote areas.

  • 349.
    Andersson, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Mazouch, Marcus
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Binary classification for predicting propensity to buy flight tickets.: A study on whether binary classification can be used to predict Scandinavian Airlines customers’ propensity to buy a flight ticket within the next seven days.2019Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A customers propensity to buy a certain product is a widely researched field and is applied in multiple industries. In this thesis it is showed that using binary classification on data from Scandinavian Airlines can predict their customers propensity to book a flight within the next coming seven days. A comparison between logistic regression and support vector machine is presented and logistic regression with reduced number of variables is chosen as the final model, due to it’s simplicity and accuracy. The explanatory variables contains exclusively booking history, whilst customer demographics and search history is showed to be insignificant.

  • 350.
    Andersson, Mathilda
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Biochar removal of micropollutants in wastewater effluentsfrom Morocco and South Africa2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
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