umu.sePublikationer
Ändra sökning
Avgränsa sökresultatet
1234567 51 - 100 av 13322
RefereraExporteraLänk till träfflistan
Permanent länk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Träffar per sida
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Författare A-Ö
  • Författare Ö-A
  • Titel A-Ö
  • Titel Ö-A
  • Publikationstyp A-Ö
  • Publikationstyp Ö-A
  • Äldst först
  • Nyast först
  • Skapad (Äldst först)
  • Skapad (Nyast först)
  • Senast uppdaterad (Äldst först)
  • Senast uppdaterad (Nyast först)
  • Disputationsdatum (tidigaste först)
  • Disputationsdatum (senaste först)
  • Standard (Relevans)
  • Författare A-Ö
  • Författare Ö-A
  • Titel A-Ö
  • Titel Ö-A
  • Publikationstyp A-Ö
  • Publikationstyp Ö-A
  • Äldst först
  • Nyast först
  • Skapad (Äldst först)
  • Skapad (Nyast först)
  • Senast uppdaterad (Äldst först)
  • Senast uppdaterad (Nyast först)
  • Disputationsdatum (tidigaste först)
  • Disputationsdatum (senaste först)
Markera
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 51.
    Adhikari, Deepak
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Flohr, Gilian
    Hogeschool Leiden, Zernikedreef 11,2333 CK Leiden, The Netherlands.
    Gorre, Nagaraju
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Shen, Yan
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Yang, Hairu
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Lundin, Eva
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi.
    Lan, Zijian
    University of Louisville Health Sciences Center, Louisville, Kentucky, USA.
    Liu, Kui
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Disruption of Tsc2 in oocytes leads to overactivation of the entire pool of primordial follicles2009Ingår i: Molecular human reproduction, ISSN 1360-9947, E-ISSN 1460-2407, Vol. 15, nr 12, s. 765-770Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To maintain the length of reproductive life in a woman, it is essential that most of her ovarian primordial follicles are maintained in a quiescent state to provide a continuous supply of oocytes. However, our understanding of the molecular mechanisms that control the quiescence and activation of primordial follicles is still in its infancy. In this study, we provide some genetic evidence to show that the tumor suppressor tuberous sclerosis complex 2 (Tsc2), which negatively regulates mammalian target of rapamycin complex 1 (mTORC1), functions in oocytes to maintain the dormancy of primordial follicles. In mutant mice lacking the Tsc2 gene in oocytes, the pool of primordial follicles is activated prematurely due to elevated mTORC1 activity in oocytes. This results in depletion of follicles in early adulthood, causing premature ovarian failure (POF). Our results suggest that the Tsc1-Tsc2 complex mediated suppression of mTORC1 activity is indispensable for maintenance of the dormancy of primordial follicles, thus preserving the follicular pool, and that mTORC1 activity in oocytes promotes follicular activation. Our results also indicate that deregulation of Tsc/mTOR signaling in oocytes may cause pathological conditions of the ovary such as infertility and POF.

  • 52. Adhikary, N C
    et al.
    Misra, Amar P
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Bailung, H
    Chutia, J
    Ion-beam driven dust ion-acoustic solitary waves in dusty plasmas2010Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 17, nr 4, artikel-id 044502Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The nonlinear propagation of small but finite amplitude dust ion-acoustic waves (DIAWs) in an ion-beam driven plasma consisting of Boltzmannian electrons, positive ions, and stationary negatively charged dust grains is studied by using the standard reductive perturbation technique. It is shown that there exist two critical values (γc1) and (γc2) of ion beam to ion phase velocity ratio (γ), above and below which the beam generated solitons are not possible. The effects of the parameters, namely, γ, the ratio of the ion beam to plasma ion density (μi), the dust to ion density ratio (μd), and the ion beam to plasma ion mass ratio (μ) on both the amplitude and width of the stationary DIAWs, are analyzed numerically, and applications of the results to laboratory ion beam as well as space plasmas (e.g., auroral plasmas) are explained.

  • 53.
    Adjeiwaah, Mary
    Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper.
    Quality assurance for magnetic resonance imaging (MRI) in radiotherapy2017Licentiatavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Magnetic resonance imaging (MRI) utilizes the magnetic properties of tissues to generate image-forming signals. MRI has exquisite soft-tissue contrast and since tumors are mainly soft-tissues, it offers improved delineation of the target volume and nearby organs at risk. The proposed Magnetic Resonance-only Radiotherapy (MR-only RT) work flow allows for the use of MRI as the sole imaging modality in the radiotherapy (RT) treatment planning of cancer. There are, however, issues with geometric distortions inherent with MR image acquisition processes. These distortions result from imperfections in the main magnetic field, nonlinear gradients, as well as field disturbances introduced by the imaged object. In this thesis, we quantified the effect of system related and patient-induced susceptibility geometric distortions on dose distributions for prostate as well as head and neck cancers. Methods to mitigate these distortions were also studied.

    In Study I, mean worst system related residual distortions of 3.19, 2.52 and 2.08 mm at bandwidths (BW) of 122, 244 and 488 Hz/pixel up to a radial distance of 25 cm from a 3T PET/MR scanner was measured with a large field of view (FoV) phantom. Subsequently, we estimated maximum shifts of 5.8, 2.9 and 1.5 mm due to patient-induced susceptibility distortions. VMAT-optimized treatment plans initially performed on distorted CT (dCT) images and recalculated on real CT datasets resulted in a dose difference of less than 0.5%.

     The magnetic susceptibility differences at tissue-metallic,-air and -bone interfaces result in local B0 magnetic field inhomogeneities. The distortion shifts caused by these field inhomogeneities can be reduced by shimming.  Study II aimed to investigate the use of shimming to improve the homogeneity of local  B0 magnetic field which will be beneficial for radiotherapy applications. A shimming simulation based on spherical harmonics modeling was developed. The spinal cord, an organ at risk is surrounded by bone and in close proximity to the lungs may have high susceptibility differences. In this region, mean pixel shifts caused by local B0 field inhomogeneities were reduced from 3.47±1.22 mm to 1.35±0.44 mm and 0.99±0.30 mm using first and second order shimming respectively. This was for a bandwidth of 122 Hz/pixel and an in-plane voxel size of 1×1 mm2.  Also examined in Study II as in Study I was the dosimetric effect of geometric distortions on 21 Head and Neck cancer treatment plans. The dose difference in D50 at the PTV between distorted CT and real CT plans was less than 1.0%.

    In conclusion, the effect of MR geometric distortions on dose plans was small. Generally, we found patient-induced susceptibility distortions were larger compared with residual system distortions at all delineated structures except the external contour. This information will be relevant when setting margins for treatment volumes and organs at risk.  

    The current practice of characterizing MR geometric distortions utilizing spatial accuracy phantoms alone may not be enough for an MR-only radiotherapy workflow. Therefore, measures to mitigate patient-induced susceptibility effects in clinical practice such as patient-specific correction algorithms are needed to complement existing distortion reduction methods such as high acquisition bandwidth and shimming.

  • 54.
    Adler, Robert
    et al.
    Umeå universitet, Samhällsvetenskapliga fakulteten, Institutionen för informatik.
    Eriksson, Andreas
    Umeå universitet, Samhällsvetenskapliga fakulteten, Institutionen för informatik.
    Visuella Effekter Inom Genrespecifik Musikvideoproduktion2010Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Today almost every artist has a music video. With today’s technology it has become a lot easier for smaller companies or amateur filmers to produce and distribute their work. But how important is an artist’s music video and where do people find their music these days? Other questions we wanted to answer were if there is a typical way a music video looks like based on its genre. And is it possible to break these stereotypical ways of producing music videos and thereby create a higher level of enjoyment from the viewer? Our main idea of achieving this was by the use of visual effects in a genre, which in our opinion usually don’t showcase these types of effects. The genre we decided to work with was singer/songwriter, which we think is one genre that doesn’t typically use visual effects. To back up our opinions we studied a lot of music videos from different genres to really see what was typical for each of them. Furthermore we made a survey to find answers for our questions about people’s views on the importance of a well-made music video and where they watch and find them. After we had found some of our answers we produced a music video, one with, and one without visual effects. We then showed these to a number of people and asked them questions about their opinions. Based on our results from studying different music videos and the surveys we came up with a conclusion. And we can say that using visual effects in a genre were they typically aren’t used is possible and it can enhance a viewers enjoyment of the music video. Although we also found out that it should be done with moderation and in good relations with the specific genre.

  • 55.
    Adlerborn, Björn
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Parallel Algorithms and Library Software for the Generalized Eigenvalue Problem on Distributed Memory Computer Systems2016Licentiatavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    We present and discuss algorithms and library software for solving the generalized non-symmetric eigenvalue problem (GNEP) on high performance computing (HPC) platforms with distributed memory. Such problems occur frequently in computational science and engineering, and our contributions make it possible to solve GNEPs fast and accurate in parallel using state-of-the-art HPC systems. A generalized eigenvalue problem corresponds to finding scalars y and vectors x such that Ax = yBx, where A and B are real square matrices. A nonzero x that satisfies the GNEP equation is called an eigenvector of the ordered pair (A,B), and the scalar y is the associated eigenvalue. Our contributions include parallel algorithms for transforming a matrix pair (A,B) to a generalized Schur form (S,T), where S is quasi upper triangular and T is upper triangular. The eigenvalues are revealed from the diagonals of S and T. Moreover, for a specified set of eigenvalues an associated pair of deflating subspaces can be computed, which typically is requested in various applications. In the first stage the matrix pair (A,B) is reduced to a Hessenberg-triangular form (H,T), where H is upper triangular with one nonzero subdiagonal and T is upper triangular, in a finite number of steps. The second stage reduces the matrix pair further to generalized Schur form (S,T) using an iterative QZ-based method. Outgoing from a one-stage method for the reduction from (A,B) to (H,T), a novel parallel algorithm is developed. In brief, a delayed update technique is applied to several partial steps, involving low level operations, before associated accumulated transformations are applied in a blocked fashion which together with a wave-front task scheduler makes the algorithm scale when running in a parallel setting. The potential presence of infinite eigenvalues makes a generalized eigenvalue problem ill-conditioned. Therefore the parallel algorithm for the second stage, reduction to (S,T) form, continuously scan for and robustly deflate infinite eigenvalues. This will reduce the impact so that they do not interfere with other real eigenvalues or are misinterpreted as real eigenvalues. In addition, our parallel iterative QZ-based algorithm makes use of multiple implicit shifts and an aggressive early deflation (AED) technique, which radically speeds up the convergence. The multi-shift strategy is based on independent chains of so called coupled bulges and computational windows which is an important source of making the algorithm scalable. The parallel algorithms have been implemented in state-of-the-art library software. The performance is demonstrated and evaluated using up to 1600 CPU cores for problems with matrices as large as 100000 x 100000. Our library software is described in a User Guide. The software is, optionally, tunable via a set of parameters for various thresholds and buffer sizes etc. These parameters are discussed, and recommended values are specified which should result in reasonable performance on HPC systems similar to the ones we have been running on.

  • 56.
    Adlerborn, Björn
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Karlsson, Lars
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Kågström, Bo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Distributed one-stage Hessenberg-triangular reduction with wavefront scheduling2018Ingår i: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 40, nr 2, s. C157-C180Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A novel parallel formulation of Hessenberg-triangular reduction of a regular matrix pair on distributed memory computers is presented. The formulation is based on a sequential cacheblocked algorithm by K degrees agstrom et al. [BIT, 48 (2008), pp. 563 584]. A static scheduling algorithm is proposed that addresses the problem of underutilized processes caused by two-sided updates of matrix pairs based on sequences of rotations. Experiments using up to 961 processes demonstrate that the new formulation is an improvement of the state of the art and also identify factors that limit its scalability.

  • 57.
    Adlerborn, Björn
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Kågström, Bo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Karlsson, Lars
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Distributed one-stage Hessenberg-triangular reduction with wavefront scheduling2016Rapport (Övrigt vetenskapligt)
    Abstract [en]

    A novel parallel formulation of Hessenberg-triangular reduction of a regular matrix pair on distributed memory computers is presented. The formulation is based on a sequential cache-blocked algorithm by Kågstrom, Kressner, E.S. Quintana-Ortí, and G. Quintana-Ortí (2008). A static scheduling algorithm is proposed that addresses the problem of underutilized processes caused by two-sided updates of matrix pairs based on sequences of rotations. Experiments using up to 961 processes demonstrate that the new algorithm is an improvement of the state of the art but also identifies factors that currently limit its scalability.

  • 58.
    Adlerborn, Björn
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Kågström, Bo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Kressner, Daniel
    A parallel QZ algorithm for distributed memory HPC systems2014Ingår i: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 36, nr 5, s. C480-C503Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Appearing frequently in applications, generalized eigenvalue problems represent one of the core problems in numerical linear algebra. The QZ algorithm of Moler and Stewart is the most widely used algorithm for addressing such problems. Despite its importance, little attention has been paid to the parallelization of the QZ algorithm. The purpose of this work is to fill this gap. We propose a parallelization of the QZ algorithm that incorporates all modern ingredients of dense eigensolvers, such as multishift and aggressive early deflation techniques. To deal with (possibly many) infinite eigenvalues, a new parallel deflation strategy is developed. Numerical experiments for several random and application examples demonstrate the effectiveness of our algorithm on two different distributed memory HPC systems.

  • 59.
    Adlerborn, Björn
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Kågström, Bo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för datavetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Högpresterande beräkningscentrum norr (HPC2N).
    Kressner, Daniel
    SB–MATHICSE–ANCHP, EPF Lausanne.
    PDHGEQZ user guide2015Rapport (Övrigt vetenskapligt)
    Abstract [en]

    Given a general matrix pair (A,B) with real entries, we provide software routines for computing a generalized Schur decomposition (S, T). The real and complex conjugate pairs of eigenvalues appear as 1×1 and 2×2 blocks, respectively, along the diagonals of (S, T) and can be reordered in any order. Typically, this functionality is used to compute orthogonal bases for a pair of deflating subspaces corresponding to a selected set of eigenvalues. The routines are written in Fortran 90 and targets distributed memory machines.

  • 60. Adnan, Muhammad
    et al.
    Iqbal, Javed
    Bibi, Shamsa
    Hussain, Riaz
    Akhtar, Muhammad Nadeem
    Rashid, Muhammad Abid
    Eliasson, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ayub, Khurshid
    Fine Tuning the Optoelectronic Properties of Triphenylamine Based Donor Molecules for Organic Solar Cells2017Ingår i: Zeitschrift fur physikalische Chemie (Munchen. 1991), ISSN 0942-9352, Vol. 231, nr 6, s. 1127-1139Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Geometrical parameters, electronic structures and photophysical properties of three new triphenylamine (TPA) and diphenylamine (DPA) based electron donor materials M1-M3 (for organic solar cells) have been investigated through density functional theory (DFT) methods at the B3LYP/6-31G(d) level of the theory. TPA and DPA are used as donor moieties due to their electron donating ability while benzothiazole, cyanide and cyanomethylacetate (CMA) moieties have been taken as acceptor moieties. The time dependent-DFT (TD-DFT) method has been employed [TD-B3LYP/6-31G (d)] for the computation of excited state properties in the gas phase and in solvent (chloroform). The polarization continuum model is applied for calculations in the solvent phase. The designed molecules exhibited broad absorption in the visible and near infra-red region of spectrum with respect to a reference molecule "R" of a similar class of compounds. Based on reorganization energies calculations, these materials could act as excellent hole transport materials.

  • 61.
    Adolfsson, David
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Claesson, Tom
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Estimation methods for Asian Quanto Basket options2019Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    All financial institutions that provide options to counterparties will in most cases get involved withMonte Carlo simulations. Options with a payoff function that depends on asset’s value at differenttime points over its lifespan are so called path dependent options. This path dependency impli-cates that there exists no parametric solution and the price must hence be estimated, it is hereMonte Carlo methods come into the picture. The problem though with this fundamental optionpricing method is the computational time. Prices fluctuate continuously on the open market withrespect to different risk factors and since it’s impossible to re-evaluate the option for all shifts dueto its computing intensive nature, estimations of the option price must be used. Estimating theprice from known points will of course never produce the same result as a full re-evaluation but anestimation method that produces reliable results and greatly reduces computing time is desirable.This thesis will evaluate different approaches and try to minimize the estimation error with respectto a certain number of risk factors.This is the background for our master thesis at Swedbank. The goal is to create multiple estima-tion methods and compare them to Swedbank’s current estimation model. By doing this we couldpotentially provide Swedbank with improvement ideas regarding some of its option products andrisk measurements. This thesis is primarily based on two estimation methods that estimate optionprices with respect to two variable risk factors, the value of the underlying assets and volatility.The first method is a grid that uses a second order Taylor expansion and the sensitivities delta,gamma and vega. The other method uses a grid of pre-simulated option prices for different shiftsin risk factors. The interpolation technique that is used in this method is calledPiecewise CubicHermiteinterpolation. The methods (or referred to as approaches in the report) are implementedto handle a relative change of 50 percent in the underlying asset’s index value, which is the firstrisk factor. Concerning the second risk factor, volatility, both methods estimate prices for a 50percent relative downward change and an upward change of 400 percent from the initial volatility.Should there emerge even more extreme market conditions both methods use linear extrapolationto estimate a new option price.

  • 62. Aeinehband, Shahin
    et al.
    Brenner, Philip
    Stahl, Sara
    Bhat, Maria
    Fidock, Mark D.
    Khademi, Mohsen
    Olsson, Tomas
    Engberg, Goran
    Jokinen, Jussi
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk vetenskap, Psykiatri.
    Erhardt, Sophie
    Piehl, Fredrik
    Cerebrospinal fluid kynurenines in multiple sclerosis: relation to disease course and neurocognitive symptoms2016Ingår i: Brain, behavior, and immunity, ISSN 0889-1591, E-ISSN 1090-2139, Vol. 51, s. 47-55Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative disease of the central nervous system, with a high rate of neurocognitive symptoms for which the molecular background is still uncertain. There is accumulating evidence for dysregulation of the kynurenine pathway (KP) in different psychiatric and neurodegenerative conditions. We here report the first comprehensive analysis of cerebrospinal fluid (CSF) kynurenine metabolites in MS patients of different disease stages and in relation to neurocognitive symptoms. Levels of tryptophan (TRP), kynurenine (KYN), kynurenic acid (KYNA) and quinolinic acid (QUIN) were determined with liquid chromatography mass spectrometry in cell-free CSF. At the group level MS patients (cohort 1; n = 71) did not differ in absolute levels of TRP, KYN, KYNA or QUIN as compared to non-inflammatory neurological disease controls (n = 20). Stratification of patients into different disease courses revealed that both absolute QUIN levels and the QUIN/KYN ratio were increased in relapsing-remitting MS (RRMS) patients in relapse. Interestingly, secondary progressive MS (SPMS) displayed a trend for lower TRP and KYNA, while primary progressive (PPMS) patients displayed increased levels of all metabolites, similar to a group of inflammatory neurological disease controls (n = 13). In the second cohort (n = 48), MS patients with active disease and short disease duration were prospectively evaluated for neuropsychiatric symptoms. In a supervised multivariate analysis using orthogonal projection to latent structures (OPLS-DA) depressed patients displayed higher KYNA/TRP and KYN/TRP ratios, mainly due to low TRP levels. Still, this model had low predictive value and could not completely separate the clinically depressed patients from the non-depressed MS patients. No correlation was evident for other neurocognitive measures. Taken together these results demonstrate that clinical disease activity and differences in disease courses are reflected by changes in KP metabolites. Increased QUIN levels of RRMS patients in relapse and generally decreased levels of TRP in SPMS may relate to neurotoxicity and failure of remyelination, respectively. In contrast, PPMS patients displayed a more divergent pattern more resembling inflammatory conditions such as systemic lupus erythematosus. The pattern of KP metabolites in RRMS patients could not predict neurocognitive symptoms.

  • 63. Aeppli, Christoph
    et al.
    Tysklind, Mats
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Holmstrand, Henry
    Gustafsson, Örjan
    Use of Cl and C Isotopic Fractionation to Identify Degradation and Sources of Polychlorinated Phenols: Mechanistic Study and Field Application2013Ingår i: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 47, nr 2, s. 790-797Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The widespread use of chlorinated phenols (CPs) as a wood preservative has led to numerous contaminated sawmill sites. However, it remains challenging to assess the extent of in situ degradation of CPs. We evaluated the use of compound-specific chlorine and carbon isotope analysis (Cl- and C-CSIA) to assess CP biotransformation. In a laboratory system, we measured isotopic fractionation during oxidative 2,4,6-trichlorophenol dechlorination by representative soil enzymes (C. fumago chloroperoxidase, horseradish peroxidase, and laccase from T. versicolor). Using a mathematical model, the validity of the Rayleigh approach to evaluate apparent kinetic isotope effects (AKIE) was confirmed. A small but significant Cl-AKIE of 1.0022 ± 0.0006 was observed for all three enzymes, consistent with a reaction pathway via a cationic radical species. For carbon, a slight inverse isotope effect was observed (C-AKIE = 0.9945 ± 0.0019). This fractionation behavior is clearly distinguishable from reported reductive dechlorination mechanisms. Based on these results we then assessed degradation and apportioned different types of technical CP mixtures used at two former sawmill sites. To our knowledge, this is the first study that makes use of two-element CSIA to study sources and transformation of CPs in the environment.

  • 64. Aerts, R.
    et al.
    Callaghan, T. V.
    Dorrepaal, E.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Systems Ecology, Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands.
    van Logtestijn, R. S. P.
    Cornelissen, J. H. C.
    Seasonal climate manipulations have only minor effects on litter decomposition rates and N dynamics but strong effects on litter P dynamics of sub-arctic bog species2012Ingår i: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 170, nr 3, s. 809-819Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Litter decomposition and nutrient mineralization in high-latitude peatlands are constrained by low temperatures. So far, little is known about the effects of seasonal components of climate change (higher spring and summer temperatures, more snow which leads to higher winter soil temperatures) on these processes. In a 4-year field experiment, we manipulated these seasonal components in a sub-arctic bog and studied the effects on the decomposition and N and P dynamics of leaf litter of Calamagrostis lapponica, Betula nana, and Rubus chamaemorus, incubated both in a common ambient environment and in the treatment plots. Mass loss in the controls increased in the order Calamagrostis < Betula < Rubus. After 4 years, overall mass loss in the climate-treatment plots was 10 % higher compared to the ambient incubation environment. Litter chemistry showed within each incubation environment only a few and species-specific responses. Compared to the interspecific differences, they resulted in only moderate climate treatment effects on mass loss and these differed among seasons and species. Neither N nor P mineralization in the litter were affected by the incubation environment. Remarkably, for all species, no net N mineralization had occurred in any of the treatments during 4 years. Species differed in P-release patterns, and summer warming strongly stimulated P release for all species. Thus, moderate changes in summer temperatures and/or winter snow addition have limited effects on litter decomposition rates and N dynamics, but summer warming does stimulate litter P release. As a result, N-limitation of plant growth in this sub-arctic bog may be sustained or even further promoted.

  • 65.
    af Klintberg, Max
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Predictive Modeling of Emissions: Heavy Duty Vehicles2016Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 66.
    Afvander, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Development of a working method for the study of a distillation process: Distillation of a multicomponent system2015Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 67.
    Aghbolagh, Mahdi Shahmohammadi
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Meynaq, Mohammad Yaser Khani
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Shimizu, Kenichi
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Lindholm-Sethson, Britta
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Aspects on mediated glucose oxidation at a supported cubic phase2017Ingår i: Bioelectrochemistry, ISSN 1567-5394, E-ISSN 1878-562X, Vol. 118, s. 8-13Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A supported liquid crystalline cubic phase housing glucose oxidase on an electrode surface has been suggested as bio-anode in a biofuel. The purpose of this investigation is to clarify some aspect on the mediated enzymatic oxidation of glucose in such a bio-anode where the mediator ferrocene-carboxylic acid and glucose were dissolved in the solution. The enzyme glucose oxidase was housed in the water channels of the mono-olein cubic phase. The system was investigated with cyclic voltammetry at different scan rates and the temperature was varied between 15 degrees C and 30 degrees C. The diffusion coefficient of the mediator and also the film resistance was estimated showing a large decrease in the mass-transport properties as the temperature was decreased. The current from mediated oxidation of glucose at the electrode surface increased with decreasing film thickness. The transport of the mediator in the cubic phase was the rate-limiting step in the overall reaction, where the oxidation of glucose took place at the outer surface of the cubic phase.

  • 68.
    Aglar, Öznur
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Design and synthesis of inhibitors of the ADP ribosylating toxin ExoS: Targeting the Type III Secretion System (T3SS) of Pseudomonas aeruginosa.2016Självständigt arbete på avancerad nivå (magisterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 69.
    Agnemo, Elin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Avfall från dricksvattenkvalitetslaboratorium: En studie om avfallsklassning och hantering av m-Endo agar LES vid Stockholm Vatten.2014Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The purpose of the study was to determine how the waste from m-Endo agar LES (LesEndo) should be categorized and managed, due to its content of the carcinogenic substance basic red 9 in basic fuchsine. The information was obtained by studying legislation and a laboratory practical was performed to verify, if basic fuchsine could remain in LesEndo agar after being heated. This was important to know for the further interpretation how to categorize and manage the waste according to the legislation. LesEndo agar was autoclaved at 121 °C for 15 and 30 minutes. E. coli and coliform bacteria was put to grow on the LesEndo agar. The results from the study showed that all replicas had coliform colonies, which appeared with a metallic fuchsine-sheen. This verified that basic fuchsine was unchanged and that there was no significant difference in growth between replicas with heated agar and the control. The total concentration of basic fuchsine in LesEndo agar was 0.08%. To be categorized as hazardous waste the threshold value for basic red 9 is 0.1%. According to a strict interpretation of the legislation, waste from used LesEndo agar should not be categorized and managed as hazardous waste. However, evaporation has to be taken into consideration and the concentration may be above 0.1%. Therefore my evaluation is that waste from used LesEndo agar should be categorized and managed as hazardous waste to protect humans and the environment from being harmed.

  • 70.
    Agnemo, Roland
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten.
    Ligniners reaktioner med alkalisk väteperoxid1981Doktorsavhandling, monografi (Övrigt vetenskapligt)
    Abstract [en]

    Under alkaline conditions hydrogen peroxide can be used either as a 1ignin-degrading or a 1ignin-preserving bleaching agent. If heavy metal ions are present and/or silicate is absent in the reaction medium, hydrogen peroxide decomposes via hydroxyl radicals and superoxide ions to oxygen and water. These decomposition products are able to react for example with phenolic lignin structures and thereby cause a partial degradation of lignin. In such a system peroxide could act as a bleaching and delignifying agent at the same time and these properties can be utilized for the bleaching of chemical pulps.In order to elucidate the factors which influence the degradation of phenolic structures by oxidation with alkaline hydrogen peroxide the lignin model compounds-methylsyringyl alcohol was studied.By determining the first order reaction rate constants for the oxidation, the main results which were obtained indicate that phenolic lignin structures can be efficiently degraded especially if:A. The pH in the bleaching liquor is close to the pK -valueàfor hydrogen peroxide.B. The ionic strength in the bleaching medium is as high as possible.C. A fixed amount of heavy metal ions (manganese) is added to the bleaching liquor.In the presence of silicate and diethylentriaminepenta-acetic acid (DTPA) hydrogen peroxide is stabilized against decomposition. Under these conditions alkaline hydrogen peroxide is able to react only with lignin units containing conjugated carbonyl groups such as quinone, aryl-oe-carbonyl and cinnamaldehyd structures, leading to an elimination of the chromophoric structures without any substantial dissolution of lignin. In this part of work we have elucidated the kinetic behavior and the reaction products from lignin model compounds of the aryl-of- carbonyl and cinnamaldehyde types.1,2-Diarylpropan-1,3,-diol structures constitute an important building unit in native lignins. We have demonstrated that under hydrogen peroxide bleaching conditions the model compound 2,3--bis(4-hydroxy-3-methoxyphenyl)-3-ethoxy-propanol was converted to stilbenes, ûe. structures which when present in pulps may contribute to a rapid yellowing. The results obtained with model compounds under simulated lignin retaining bleaching conditions demonstrate that there are possibilities to improve the bleaching of mechanical pulps with hydrogen peroxide if:A. The remaining heavy metal ions complexed with DTPA are present in their lowest valence states.B. The concentration of hydroperoxy ions can be maintained at a high level at the lowest possible pH-value.

  • 71. Agostinelli, Marta
    et al.
    Cleary, Michelle
    Martin, Juan A.
    Albrectsen, Benedicte R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Witzell, Johanna
    Pedunculate Oaks (Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity2018Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikel-id 1758Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ecological significance of trees growing in urban and peri-urban settings is likely to increase in future land-use regimes, calling for better understanding of their role as potential reservoirs or stepping stones for associated biodiversity. We studied the diversity of fungal endophytes in woody tissues of asymptomatic even aged pedunculate oak trees, growing as amenity trees in a peri-urban setting. The trees were classified into three groups according to their phenotypic vitality (high, medium, and low). Endophytes were cultured on potato dextrose media from surface sterilized twigs and DNA sequencing was performed to reveal the taxonomic identity of the morphotypes. In xylem tissues, the frequency and diversity of endophytes was highest in oak trees showing reduced vitality. This difference was not found for bark samples, in which the endophyte infections were more frequent and communities more diverse than in xylem. In general, most taxa were shared across the samples with few morphotypes being recovered in unique samples. Leaf phenolic profiles were found to accurately classify the trees according to their phenotypic vitality. Our results confirm that xylem is more selective substrate for endophytes than bark and that endophyte assemblages in xylem are correlated to the degree of host vitality. Thus, high vitality of trees may be associated with reduced habitat quality to wood-associated endophytes.

  • 72. Agrawal, Ganesh Kumar
    et al.
    Job, Dominique
    Kieselbach, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Barkla, Bronwyn J.
    Chen, Sixue
    Deswal, Renu
    Luethje, Sabine
    Amalraj, Ramesh Sundar
    Tanou, Georgia
    Ndimba, Bongani Kaiser
    Cramer, Rainer
    Weckwerth, Wolfram
    Wienkoop, Stefanie
    Dunn, Michael J.
    Kim, Sun Tae
    Fukao, Yochiro
    Yonekura, Masami
    Zolla, Lello
    Rohila, Jai Singh
    Waditee-Sirisattha, Rungaroon
    Masi, Antonio
    Wang, Tai
    Sarkar, Abhijit
    Agrawal, Raj
    Renaut, Jenny
    Rakwal, Randeep
    INPPO Actions and Recognition as a Driving Force for Progress in Plant Proteomics: Change of Guard, INPPO Update, and Upcoming Activities2013Ingår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 13, nr 21, s. 3093-3100Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    The International Plant Proteomics Organization (INPPO) is a non-profit organization whose members are scientists involved or interested in plant proteomics. Since the publication of the first INPPO highlights in 2012, continued progress on many of the organization's mandates/goals has been achieved. Two major events are emphasized in this second INPPO highlights. First, the change of guard at the top, passing of the baton from Dominique Job, INPPO founding President to Ganesh Kumar Agrawal as the incoming President. Ganesh K. Agrawal, along with Dominique Job and Randeep Rakwal initiated the INPPO. Second, the most recent INPPO achievements and future targets, mainly the organization of first the INPPO World Congress in 2014, tentatively planned for Hamburg (Germany), are mentioned.

  • 73. Agugiaro, G.
    et al.
    Remondino, F.
    Girardi, G.
    von Schwerin, J.
    Richards-Rissetto, Heather
    Umeå universitet, Humanistiska fakulteten, Humlab.
    De Amicis, R.
    A web-based interactive tool for multi-resolution 3d models of a maya archaeological site2011Ingår i: 4TH ISPRS INTERNATIONAL WORKSHOP 3D-ARCH 2011: 3D VIRTUAL RECONSTRUCTION AND VISUALIZATION OF COMPLEX ARCHITECTURES / [ed] Remondino, F; ElHakim, S, 2011, nr W16, s. 23-30Konferensbidrag (Refereegranskat)
    Abstract [en]

    Continuous technological advances in surveying, computing and digital-content delivery are strongly contributing to a change in the way Cultural Heritage is "perceived": new tools and methodologies for documentation, reconstruction and research are being created to assist not only scholars, but also to reach more potential users (e.g. students and tourists) willing to access more detailed information about art history and archaeology. 3D computer-simulated models, sometimes set in virtual landscapes, offer for example the chance to explore possible hypothetical reconstructions, while on-line GIS resources can help interactive analyses of relationships and change over space and time. While for some research purposes a traditional 2D approach may suffice, this is not the case for more complex analyses concerning spatial and temporal features of architecture, like for example the relationship of architecture and landscape, visibility studies etc. The project aims therefore at creating a tool, called "QueryArch3D" tool, which enables the web-based visualisation and queries of an interactive, multi-resolution 3D model in the framework of Cultural Heritage. More specifically, a complete Maya archaeological site, located in Copan (Honduras), has been chosen as case study to test and demonstrate the platform's capabilities. Much of the site has been surveyed and modelled at different levels of detail (LoD) and the geometric model has been semantically segmented and integrated with attribute data gathered from several external data sources. The paper describes the characteristics of the research work, along with its implementation issues and the initial results of the developed prototype. [GRAPHICS] .

  • 74. Aguiar, Francisca C.
    et al.
    Segurado, Pedro
    Martins, Maria Joao
    Bejarano, Maria Dolores
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Nilsson, Christer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Portela, Maria Manuela
    Merritt, David M.
    The abundance and distribution of guilds of riparian woody plants change in response to land use and flow regulation2018Ingår i: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 55, nr 5, s. 2227-2240Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    1. Many riparian ecosystems in Mediterranean Europe are affected by land use and flow alteration by dams. We focused on understanding how these stressors and their components affect riparian forests in the region. We asked the following questions: (1) Are there well‐defined, responsive riparian guilds? (2) Do dam‐induced streamflows determine abundance and distribution of riparian guilds? (3) What are the main drivers governing composition and cover of riparian guilds in regulated rivers?

    2. We inventoried the cover of riparian woody species in free‐flowing rivers and downstream of dams. We performed a cluster analysis and ordination to derive riparian guilds, using abundance data from 66 riparian woody species and 26 functional plant traits. We used a reduced set of principal components for the environment, land use and hydrology, and general linear modelling to explore the effect of these factors (separately and combined) on riparian guilds.

    3. We found that: (1) four dominant guilds are responsive to disturbance in southwestern European streams, namely the obligate riparian, water‐stress tolerant, deciduous competitive and Mediterranean evergreen guilds; (2) a set of land use and hydrological variables differentially affect the diverse co‐occurring riparian guilds; (3) frequency and duration of high flow pulses and the low‐flow conditions were major drivers of change in landscapes dominated by intensive agriculture and forestry; (4) storage reservoirs reduced the cover of obligate riparian and Mediterranean evergreen guilds, and increased the abundance of water‐stress tolerant and deciduous competitive guilds, while run‐of‐river dams, having limited water storage, reduced both obligate and deciduous competitive guilds.

    4. Synthesis and applications. Future research in southwestern Europe should address the resilience of riparian guilds and the effects of interacting landscape factors and stressors on guild distribution. Streamflow regulations downstream of reservoirs should focus on specific flow components, namely the magnitude of flows, and frequency and duration of extreme flow events. For successful mitigation of the dam‐induced effects on riparian vegetation, river management plans must incorporate the environmental and land use site‐specific contexts.

  • 75.
    Aguilar, Ximena
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Folding and interaction studies of subunits in protein complexes2014Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Proteins function as worker molecules in the cell and their natural environment is crowded. How they fold in a cell-like environment and how they recognize their interacting partners in such conditions, are questions that underlie the work of this thesis.

    Two distinct subjects were investigated using a combination of biochemical- and biophysical methods. First, the unfolding/dissociation of a heptameric protein (cpn10) in the presence of the crowding agent Ficoll 70. Ficoll 70 was used to mimic the crowded environment in the cell and it has been used previously to study macromolecular crowding effects, or excluded volume effects, in protein folding studies. Second, the conformational changes upon interaction between the Mediator subunit Med25 and the transcription factor Dreb2a from Arabidopsis thaliana. Mediator is a transcriptional co-regulator complex which is conserved from yeast to humans. The molecular mechanisms of its action are however not entirely understood. It has been proposed that the Mediator complex conveys regulatory signals from promoter-bound transcription factors (activators/repressors) to the RNA polymerase II machinery through conformational rearrangements.

    The results from the folding study showed that cpn10 was stabilized in the presence of Ficoll 70 during thermal- and chemical induced unfolding (GuHCl). The thermal transition midpoint increased by 4°C, and the chemical midpoint by 0.5 M GuHCl as compared to buffer conditions. Also the heptamer-monomer dissociation was affected in the presence of Ficoll 70, the transition midpoint was lower in Ficoll 70 (3.1 μM) compared to in buffer (8.1 μM) thus indicating tighter binding in crowded conditions. The coupled unfolding/dissociation free energy for the heptamer increased by about 36 kJ/mol in Ficoll. Altogether, the results revealed that the stability effect on cpn10 due to macromolecular crowding was larger in the individual monomers (33%) than at the monomer-monomer interfaces (8%).

    The results from the interaction study indicated conformational changes upon interaction between the A. thaliana Med25 ACtivator Interaction Domain (ACID) and Dreb2a. Structural changes were probed to originate from unstructured Dreb2a and not from the Med25-ACID. Human Med25-ACID was also found to interact with the plant-specific Dreb2a, even though the ACIDs from human and A. thaliana share low sequence homology. Moreover, the human Med25-interacting transcription factor VP16 was found to interact with A. thaliana Med25. Finally, NMR, ITC and pull-down experiments showed that the unrelated transcription factors Dreb2a and

    VP16 interact with overlapping regions in the ACIDs of A. thaliana and human Med25.

    The results presented in this thesis contribute to previous reports in two different aspects. Firstly, they lend support to the findings that the intracellular environment affects the biophysical properties of proteins. It will therefore be important to continue comparing results between in vitro and cell-like conditions to measure the magnitude of such effects and to improve the understanding of protein folding and thereby misfolding of proteins in cells. Better knowledge of protein misfolding mechanisms is critical since they are associated to several neurodegenerative diseases such as Alzheimer’s and Parkinson's. Secondly, our results substantiate the notion that transcription factors are able to bind multiple targets and that they gain structure upon binding. They also show that subunits of the conserved Mediator complex, despite low sequence homologies, retain a conserved structure and function when comparing evolutionary diverged species.

  • 76.
    Aguilar, Ximena
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Blomberg, Jeanette
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Brännström, Kristoffer
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Olofsson, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Schleucher, Jurgen
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Björklund, Stefan
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Interaction Studies of the Human and Arabidopsis thaliana Med25-ACID Proteins with the Herpes Simplex Virus VP16-and Plant-Specific Dreb2a Transcription Factors2014Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 5, s. e98575-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Mediator is an evolutionary conserved multi-protein complex present in all eukaryotes. It functions as a transcriptional coregulator by conveying signals from activators and repressors to the RNA polymerase II transcription machinery. The Arabidopsis thaliana Med25 (aMed25) ACtivation Interaction Domain (ACID) interacts with the Dreb2a activator which is involved in plant stress response pathways, while Human Med25-ACID (hMed25) interacts with the herpes simplex virus VP16 activator. Despite low sequence similarity, hMed25-ACID also interacts with the plant-specific Dreb2a transcriptional activator protein. We have used GST pull-down-, surface plasmon resonance-, isothermal titration calorimetry and NMR chemical shift experiments to characterize interactions between Dreb2a and VP16, with the hMed25 and aMed25-ACIDs. We found that VP16 interacts with aMed25-ACID with similar affinity as with hMed25-ACID and that the binding surface on aMed25-ACID overlaps with the binding site for Dreb2a. We also show that the Dreb2a interaction region in hMed25-ACID overlaps with the earlier reported VP16 binding site. In addition, we show that hMed25-ACID/Dreb2a and aMed25-ACID/Dreb2a display similar binding affinities but different binding energetics. Our results therefore indicate that interaction between transcriptional regulators and their target proteins in Mediator are less dependent on the primary sequences in the interaction domains but that these domains fold into similar structures upon interaction.

  • 77.
    Aguilar, Ximena
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Weise, Christoph
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sparrman, Tobias
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wolf-Watz, Magnus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Wittung-Stafshede, Pernilla
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Macromolecular crowding extended to a heptameric system: the co-chaperonin protein 102011Ingår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 50, nr 14, s. 3034-3044Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Experiments on monomeric proteins have shown that macromolecular crowding can stabilize toward heat perturbation and also modulate native-state structure. To assess the effects of macromolecular crowding on unfolding of an oligomeric protein, we here tested the effects of the synthetic crowding agent Ficoll 70 on human cpn10 (GroES in E. coli), a heptameric protein consisting of seven identical β-barrel subunits assembling into a ring. Using far-UV circular dichroism (CD), tyrosine fluorescence, nuclear magnetic resonance (NMR), and cross-linking experiments, we investigated thermal and chemical stability, as well as the heptamer-monomer dissociation constant, without and with crowding agent. We find that crowding shifts the heptamer-monomer equilibrium constant in the direction of the heptamer. The cpn10 heptamer is both thermally and thermodynamically stabilized in 300 mg/mL Ficoll 70 as compared to regular buffer conditions. Kinetic unfolding experiments show that the increased stability in crowded conditions, in part, is explained by slower unfolding rates. A thermodynamic cycle reveals that in presence of 300 mg/mL Ficoll the thermodynamic stability of each cpn10 monomer increases by over 30%, whereas the interfaces are stabilized by less than 10%. We also introduce a new approach to analyze the spectroscopic data that makes use of multiple wavelengths: this provides robust error estimates of thermodynamic parameters.

  • 78. Aguilera, Adriana Freites
    et al.
    Tolvanen, Pasi
    Heredia, Shuyana
    Muñoz, Marta González
    Samson, Tina
    Oger, Adrien
    Verove, Antoine
    Eränen, Kari
    Leveneur, Sebastien
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Industrial Chemistry & Reaction Engineering, Department of Chemical Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Åbo-Turku, Finland.
    Salmi, Tapio
    Epoxidation of fatty acids and vegetable oils assisted by microwaves catalyzed by a cation exchange resin2018Ingår i: Industrial & Engineering Chemistry Research, ISSN 0888-5885, E-ISSN 1520-5045, Vol. 57, nr 11, s. 3876-3886Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Epoxidation of oleic acid and cottonseed oil was conducted in a semibatch reactor with in-situ-formed percarboxylic acid (peracetic acid or perpropionic acid), using hydrogen peroxide as an oxidizing agent and carboxylic acid (acetic acid or propionic acid) as oxygen carriers. Amberlite IR-120 was implemented as the catalyst. The system was comprised of a loop reactor, where the mixture was pumped through a single-mode cavity in which microwave irradiation was introduced. A heat exchanger was integrated into the system to replace microwave heating, to compare the results obtained via microwave heating versus conventional heating. The catalyst loading effect was studied, as well as the influence of microwave irradiation and the implementation of the SpinChem rotating bed reactor (RBR), in hopes of decreasing the influence of the internal mass transfer. The application of microwave irradiation results in an improvement of the reaction yield in the absence of a catalyst.

  • 79. Aguilera, Adriana Freites
    et al.
    Tolvanen, Pasi
    Oger, Adrien
    Eränen, Kari
    Leveneur, Sébastien
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Laboratory of Industrial Chemistry and Reaction Engineering, Department of Chemical Engineering, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, Turku-Åbo, Finland.
    Salmi, Tapio
    Screening of ion exchange resin catalysts for epoxidation of oleic acid under the influence of conventional and microwave heating2019Ingår i: Journal of chemical technology and biotechnology (1986), ISSN 0268-2575, E-ISSN 1097-4660, Vol. 94, nr 9, s. 3020-3031Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: For many chemical systems, it is of great importance to find a durable, active and efficient catalyst that improves the process performance. Epoxidation of oleic acid with peracetic acid (Prilezhaev oxidation) was carried out in an isothermal loop reactor in the presence of heterogeneous catalysts. The kinetic experiments conducted under microwave heating (MW) were compared with identical experiments carried out under conventional (conductive/convective) heating. Extensive screening of heterogeneous catalysts was conducted and the influence of microwave irradiation on the reaction kinetics was studied. Several ion exchange resins were screened to explore their applicability and activity in the epoxidation of oleic acid. The perhydrolysis reaction (peracetic acid formed in situ from acetic acid and H2O2) was promoted with the use of various solid acid catalysts: Amberlite IR-120, Amberlyst 15, Smopex®, Dowex 50x8-100, Dowex 50x8-50, Dowex 50x2-100 and Nafion™.

    Results: From the selected group of catalysts, Dowex 50-x8100 and Dowex 50x8-50 produced the highest yield of epoxidized oil. Only minor differences in the reactant conversion and the product yield were found in the experiments carried out under microwave exposure compared to the conventionally heated experiments in the presence of several ion exchange resins.

    Conclusions: The catalytic effect was much more prominent than the microwave effect, because the solid acid catalysts enhanced the slow step of the process, the perhydrolysis of acetic acid. The catalytic effect was very dominant and a considerable improvement of the oleic acid conversion and the epoxide yield was observed in the presence of the top-performing catalysts.

  • 80.
    Aguilo, Francesca
    et al.
    Umeå universitet, Medicinska fakulteten, Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM). Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi. Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
    Walsh, Martin J.
    The N6-Methyladenosine RNA modification in pluripotency and reprogramming2017Ingår i: Current Opinion in Genetics and Development, ISSN 0959-437X, E-ISSN 1879-0380, Vol. 46, s. 77-82Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Chemical modifications of RNA provide a direct and rapid way to manipulate the existing transcriptome, allowing rapid responses to the changing environment further enriching the regulatory capacity of RNA. N-6-Methyladenosine(m(6)A) has been identified as the most abundant internal modification of messenger RNA in eukaryotes, linking external stimuli to an intricate network of transcriptional, post-transcriptional and translational processes. M(6)A modification affects a broad spectrum of cellular functions, including maintenance of the pluripotency of embryonic stem cells (ESCs) and the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). In this review, we summarize the most recent findings on m(6)A modification with special focus on the different studies describing how m(6)A is implicated in ESC self-renewal, cell fate specification and iPSC generation.

  • 81.
    Aguilo, Francesca
    et al.
    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
    Zakirova, Zuchra
    Nolan, Katie
    Wagner, Ryan
    Sharma, Rajal
    Hogan, Megan
    Wei, Chengguo
    Sun, Yifei
    Walsh, Martin J.
    Kelley, Kevin
    Zhang, Weijia
    Ozelius, Laurie J.
    Gonzalez-Alegre, Pedro
    Zwaka, Thomas P.
    Ehrlich, Michelle E.
    THAP1: Role in Mouse Embryonic Stem Cell Survival and Differentiation2017Ingår i: Stem Cell Reports, ISSN 2213-6711, Vol. 9, nr 1, s. 92-107Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    THAP1 (THAP [Thanatos-associated protein] domain-containing, apoptosis-associated protein 1) is a ubiquitously expressed member of a family of transcription factors with highly conserved DNA-binding and protein-interacting regions. Mutations in THAP1 cause dystonia, DYT6, a neurologic movement disorder. THAP1 downstream targets and the mechanism via which it causes dystonia are largely unknown. Here, we show that wild-type THAP1 regulates embryonic stem cell (ESC) potential, survival, and proliferation. Our findings identify THAP1 as an essential factor underlying mouse ESC survival and to some extent, differentiation, particularly neuroectodermal. Loss of THAP1 or replacement with a disease-causing mutation results in an enhanced rate of cell death, prolongs Nanog, Prdm14, and/or Rex1 expression upon differentiation, and results in failure to upregulate ectodermal genes. ChIP-Seq reveals that these activities are likely due in part to indirect regulation of gene expression.

  • 82.
    Agvik, Simon
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    A deformable terrain model in multi-domain dynamics using elastoplastic constraints: An adaptive approach2015Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Achieving realistic simulations of terrain vehicles in their work environment does not only require a careful model of the vehicle itself but the vehicle's interactions with the surroundings are equally important. For off-road ground vehicles the terrain will heavily affect the behaviour of the vehicle and thus puts great demands on the terrain model.

    The purpose of this project has been to develop and evaluate a deformable terrain model, meant to be used in real-time simulations with multi-body dynamics. The proposed approach is a modification of an existing elastoplastic model based on linear elasticity theory and a capped Drucker-Prager model, using it in an adaptive way. The original model can be seen as a system of rigid bodies connected by elastoplastic constraints, representing the terrain. This project investigates if it is possible to create dynamic bodies just when it is absolutely necessary, and store information about possible deformations in a grid.

    Two methods used for transferring information between the dynamic bodies and the grid have been evaluated; an interpolating approach and a discrete approach. The test results indicate that the interpolating approach is preferable, with better stability to an equal performance cost. However, stability problems still exist that have to be solved if the model should be useful in a commercial product.

  • 83. Ahad, Abdul
    et al.
    Keech, Olivier
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Lindén, Pernilla
    Brouwer, Bastiaan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Stenlund, Hans
    Moritz, Thomas
    Jansson, Stefan
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Comparison between leaves from darkened plants and individually-darkened leaves reveals differential metabolic strategies in response to darknessManuskript (preprint) (Övrigt vetenskapligt)
  • 84.
    Ahlbeck, Jakob
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Mosebach, Fredrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Analys av risker med garantinivåer i förhållande till förväntade utbetalningar och portföljavkastningar för traditionella pensionsförsäkringar: Ett examensarbete för Folksam Liv med dotterbolag2017Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 85.
    Ahlberg, Sebastian
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Ambjörnsson, Tobias
    Lizana, Ludvig
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA2015Ingår i: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 17, artikel-id 043036Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    30% of the DNA in E. coli bacteria is covered by proteins. Such a high degree of crowding affects the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc) in ways that are not yet fully understood. In this paper, we theoretically address the diffusion constant of a tracer particle in a one-dimensional system surrounded by impenetrable crowder particles. While the tracer particle always stays on the lattice, crowder particles may unbind to a surrounding bulk and rebind at another, or the same, location. In this scenario we determine how the long time diffusion constant D (after many unbinding events) depends on (i) the unbinding rate of crowder particles k(off), and (ii) crowder particle line density rho, from simulations (using the Gillespie algorithm) and analytical calculations. For small k(off), we find D similar to k(off)/rho(2) when crowder particles do not diffuse on the line, and D similar to root Dk(off)/rho when they are diffusing; D is the free particle diffusion constant. For large k(off), we find agreement with mean-field results which do not depend on k(off). From literature values of k(off) and D, we show that the small k(off) -limit is relevant for in vivo protein diffusion on crowded DNA. Our results apply to single-molecule tracking experiments.

  • 86.
    Ahlgren, Gunnel
    et al.
    Department of Ecology and Evolution (Limnology), Uppsala University, Uppsala, Sweden.
    Vrede, Tobias
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Goedkoop, Willem
    Department of Environmental Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Fatty Acid Ratios in Freshwater Fish, Zooplankton and Zoobenthos - Are There Specific Optima?2009Ingår i: Lipids in Aquatic Ecosystems / [ed] Martin Kainz, Michael T. Brett, Michael T. Arts, New York: Springer-Verlag New York, 2009, s. 147-178Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    Two groups of polyunsaturated fatty acids (PUFA), termed omega-3 and omega-6 in food (or here as n-3 and n-6 PUFA, respectively), are essential for all vertebrates and probably also for nearly all invertebrates. The absolute concentrations of the different PUFA are important, as is an appropriate balance between the two. The optimal ratio of n-3/n-6 is not known for most organisms but is anticipated to be more or less species-specific (Sargent et al. 1995). The three most important PUFA in vertebrates are eicosapentaenoic acid (EPA, 20:5n-3), docosahexaenoic acid (DHA, 22:6n-3) and arachidonic acid (ARA, 20:4n-6). Both EPA and ARA are precursors for biologically active eicosanoids that are vital components of cell membranes and play many dynamic roles in mediating and controlling a wide array of cellular activities (Crawford et al. 1989; Harrison 1990; Henderson et al. 1996; see Chap. 9). Since n-3 and n-6 PUFA cannot be synthesized de novo by most metazoans, they must be included in the diet, either as EPA, DHA and ARA, or as their precursors, such as α-linolenic acid (ALA, 18:3n-3, precursor of EPA and DHA) and linoleic acid (LIN, 18:2n-6, precursor of ARA) (Bell et al. 1986; Sargent et al. 1995). Both ALA and LIN are produced in the thylacoid membranes of algae and plants with chlorophyll (Sargent at al. 1987).

  • 87. Ahlgren, Joakim
    et al.
    De Brabandere, Heidi
    Reitzel, Kasper
    Rydin, Emil
    Gogoll, Adolf
    Waldeback, Monica
    Sediment phosphorus extractants for phosphorus-31 nuclear magnetic resonance analysis: A quantitative evaluation2007Ingår i: Journal of Environmental Quality, ISSN 0047-2425, E-ISSN 1537-2537, Vol. 36, nr 3, s. 892-898Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The influence of pre-extractant, extractant, and post-extractant on total extracted amounts of P and organic P compound groups measured with 31 P nuclear magnetic resonance (P-31-NMR) in lacustrine sediment was examined. The main extractants investigated were sodium hydroxide (NaOH) and sodium hydroxide ethylenediaminetetraacetic acid (NaOH-EDTA) with bicarbonate buffered dithionite (BD) or EDTA as pre-extractants. Post extractions were conducted using either NaOH or NaOH-EDTA, depending on the main extractant. Results showed that the most efficient combination of extractants for total P yield was NaOH with EDTA as pre-extractant, yielding almost 50% more than the second best procedure. The P compound groups varying the most between the different extraction procedures were polyphosphates and pyrophosphates. NaOH with BD as pre-extractant was the most efficient combination for these compound groups.

  • 88.
    Ahlgren, Joakim
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF). The Swedish Institute for the Marine Environment, PO Box 260, SE-40530 Göteborg, Sweden.
    Grimvall, Anders
    Omstedt, Anders
    Rolff, Carl
    Wikner, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF). The Swedish Institute for the Marine Environment, PO Box 260, SE-40530 Göteborg, Sweden.
    Temperature, DOC level and basin interactions explain the declining oxygen concentrations in the Bothnian Sea2017Ingår i: Journal of Marine Systems, ISSN 0924-7963, E-ISSN 1879-1573, Vol. 170, s. 22-30Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Hypoxia and oxygen deficient zones are expanding worldwide. To properly manage this deterioration of the marine environment, it is important to identify the causes of oxygen declines and the influence of anthropogenic activities. Here, we provide a study aiming to explain the declining oxygen levels in the deep waters of the Bothnian Sea over the past 20 years by investigating data from environmental monitoring programmes. The observed decline in oxygen concentrations in deep waters was found to be primarily a consequence of water temperature increase and partly caused by an increase in dissolved organic carbon (DOC) in the seawater (R-Adj(2). = 0.83) as well as inflow from the adjacent sea basin. As none of the tested eutrophication-related predictors were significant according to a stepwise multiple regression, a regional increase in nutrient inputs to the area is unlikely to explain a significant portion of the oxygen decline. Based on the findings of this study, preventing the development of anoxia in the deep water of the Bothnian Sea is dependent on the large-scale measures taken to reduce climate change. In addition, the reduction of the nutrient load to the Baltic Proper is required to counteract the development of hypoxic and phosphate-rich water in the Baltic Proper, which can form deep water in the Bothnian Sea. The relative importance of these sources to oxygen consumption is difficult to determine from the available data, but the results clearly demonstrate the importance of climate related factors such as temperature, DOC and inflow from adjacent basins for the oxygen status of the sea.

  • 89. Ahlgren, Joakim
    et al.
    Reitzel, Kasper
    Danielsson, Rolf
    Gogoll, Adolf
    Rydin, Emil
    Biogenic phosphorus in oligotrophic mountain lake sediments: Differences in composition measured with NMR spectroscopy2006Ingår i: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 40, nr 20, s. 3705-3712Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Phosphorus (P) composition in alkaline sediment extracts from three Swedish oligotrophic mountain lakes was investigated using P-31-NMR spectroscopy. Surface sediments from one natural lake and two mature reservoirs, one of which has received nutrient additions over the last 3 years, were compared with respect to biogenic P composition. The results show significant differences in the occurrence of labile and biogenic P species in the sediments of the different systems. The P compound groups that varied most between these three systems were pyrophosphate and polyphosphates, compound groups known to play an important role in sediment P recycling. The content of these compound groups was lowest in the reservoirs and may indicate a coupling between anthropogenic disturbances (i.e., impoundment) to a water system and the availability of labile P species in the sediment. A statistical study was also conducted to determine the accuracy and reliability of using P-31-NMR spectroscopy for quantification of sediment P forms. (c) 2006 Elsevier Ltd. All rights reserved.

  • 90. Ahlgren, Joakim
    et al.
    Reitzel, Kasper
    De Brabandere, Heidi
    Gogoll, Adolf
    Rydin, Emil
    Release of organic P forms from lake sediments2011Ingår i: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 45, nr 2, s. 565-572Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The effects of different physical and chemical conditions on the decomposition and release of organic and inorganic P compound groups from the sediment of Lake Erken were investigated in a series of laboratory experiments. Conditions investigated were temperature, oxygen level, and the effects of additions of carbon substrate (glucose) and poison (formalin). The effects on the P compound groups were determined by measurements with (31)P NMR before and after the experiments, as well as analysis of P in effluent water throughout the experiment. Phosphate analysis of the effluent water showed that oxygen level was the most influential in terms of release rates, with the sediments under anoxic conditions generally releasing more phosphate than the other treatments. (31)P NMR showed that the various treatments did influence the P compound group composition of the sediment. In particular, the addition of glucose led to a decrease in orthophosphate and polyphosphate while the addition of formalin led to a decrease in phosphorus lipids, DNA-phosphate and polyphosphate. Oxic conditions resulted in an increase in polyphosphates, and anoxic conditions in a decrease in these. Temperature did not seem to affect the composition significantly. (c) 2010 Elsevier Ltd. All rights reserved.

  • 91. Ahlgren, Joakim
    et al.
    Reitzel, Kasper
    Tranvik, Lars
    Gogoll, Adolf
    Rydin, Emil
    Degradation of organic phosphorus compounds in anoxic Baltic Sea sediments: A P-31 nuclear magnetic resonance study2006Ingår i: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 51, nr 5, s. 2341-2348Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The composition and abundance of phosphorus extracted by NaOH-ethylenediaminetetraacetic acid from anoxic Northwest Baltic Sea sediment was characterized and quantified using solution P-31 nuclear magnetic resonance. Extracts from sediment depths down to 55 cm, representing 85 yr of deposition, contained 18.5 g m(-2) orthophosphate. Orthophosphate monoesters, teichoic acid P, microbial P lipids, DNA P, and pyrophosphate corresponded to 6.7, 0.3, 1.1, 3.0, and 0.03 g P m(-2), respectively. The degradability of these compound groups was estimated by their decline in concentration with sediment depth. Pyrophosphate had the shortest half-life (3 yr), followed by microbial P lipids with a half-life of 5 yr, DNA P (8 yr), and orthophosphate monoesters (16 yr). No decline in concentration with sediment depth was observed for orthophosphate or teichoic acid P.

  • 92.
    Ahlgren, Joakim
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF). Havsmiljöinstitutet.
    Rolff, Carl
    Stockholms universitet.
    Grimvall, Anders
    Havsmiljöinstitutet.
    Omstedt, Anders
    Göteborgs universitet.
    Wikner, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå marina forskningscentrum (UMF). Havsmiljöinstitutet.
    Orsaker till minskande syrehalter i Bottenhavet2017Rapport (Refereegranskat)
    Abstract [sv]

    Resultat från den nationella miljöövervakningen visar att syrehalterna i Bottenhavet har minskat sedan 1970-talet, en minskning som accelererat från 1990. För att ha möjlighet att på något sätt kunna åtgärda denna försämring av den marina miljön är det nödvändigt att identifiera orsakerna till denna syreminskning, eftersom olika orsaker kan kräva olika former av åtgärder. Om orsaken till exempel är ökad syreförbrukning beroende på regional övergödning, skulle detta innebära ökat behov av regionala reningsåtgärder. Målsättningen med projektet var därmed att ge en tillförlitlig förklaring till de sjunkande syrehalterna i Bottenhavet under de senaste 20 åren genom att använda data från de nationella miljöövervakningsprogrammen. De huvudhypoteser som undersöktes som orsaker till de sjunkande syrehalterna var:  • Ökad regional gödning av Bottenhavet och därmed ökad produktion.  • Tillförsel av syrefattigt och fosfatrikt från Egentliga Östersjön.  • Starkare haloklin och försämrad ventilation av Bottenhavets djupvatten.  • Ökad temperatur och ökad tillförsel av löst organiskt kol. Analys av tidsserier och modellanalyser utifrån miljöövervaknings- och forskningsdata visade att den observerade syrehaltsminskningen i Bottenhavets djupvatten främst beror på en ökning av vattentemperaturen och delvis på en ökning av löst organiskt kol i vattnet, samt tillflöde från Egentliga Östersjön. Dataanalysen visade däremot inget tydligt stöd för att ökad produktion av biomassa i Bottenhavet orsakat de minskande syrehalterna. Detta gäller indikatorer för växtplankton, sedimentation och bakterieplankton som alla förväntas öka vid ökad produktion och det finns således inga direkta indicier för att stödja hypotesen om ökad gödning av Bottenhavet.  Sammantaget visar de analyser som gjorts inom projektet att Bottenhavets framtida hälsa främst gynnas av en kombination av åtgärder för att motverka globala klimatförändringar, samt åtgärder för att förbättra vattenkvaliteten i Egentliga Östersjön. Näringstillförsel från Bottenhavets avrinningsområden bedöms främst ha haft betydelse för syresituationen i kustnära vattenförekomster. Den bedöms därför inte i betydande omfattning ha orsakat de minskande syrehalterna i Bottenhavets utsjöområden.  

  • 93. Ahlgren, Joakim
    et al.
    Tranvik, L
    Gogoll, A
    Waldeback, M
    Markides, K
    Rydin, E
    Sediment depth attenuation of biogenic phosphorus compounds measured by P-31 NMR2005Ingår i: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 39, nr 3, s. 867-872Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Being a major cause of eutrophication and subsequent loss of water quality, the turnover of phosphorus (P) in lake sediments is in need of deeper understanding. A major part of the flux of P to eutrophic lake sediments is organically bound or of biogenic origin. This P is incorporated in a poorly described mixture of autochthonous and allochthonous sediment and forms the primary storage of P available for recycling to the water column, thus regulating lake trophic status. To identify and quantify biogenic sediment P and assess its lability, we analyzed sediment cores from Lake Erken, Sweden, using traditional P fractionation, and in parallel, NaOH extracts were analyzed using (31)p NMR. The surface sediments contain orthophosphates (ortho-P) and pyrophosphates (pyro-P), as well as phosphate mono- and diesters. The first group of compounds to disappear with increased sediment depth is pyrophosphate, followed by a steady decline of the different ester compounds. Estimated half-life times of these compound groups are about 10 yr for pyrophosphate and 2 decades for mono- and diesters. Probably, these compounds will be mineralized to ortho-P and is thus potentially available for recycling to the water column, supporting further growth of phytoplankton. In conclusion, P-31 NMR is a useful tool to asses the bioavailability of certain P compound groups, and the combination with traditional fractionation techniques makes quantification possible.

  • 94.
    Ahlgren, Per
    et al.
    Department of e-Resources, University Library, Stockholm University.
    Colliander, Cristian
    Högskolan i Jönköping, Högskolebiblioteket.
    Document-document similarity approaches and science mapping: experimental comparison of five approaches2009Ingår i: Journal of Informetrics, ISSN 1751-1577, E-ISSN 1875-5879, Vol. 3, nr 1, s. 49-63Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This paper treats document-document similarity approaches in the context of science mapping. Five approaches, involving nine methods, are compared experimentally. We compare text-based approaches, the citation-based bibliographic coupling approach, and approaches that combine text-based approaches and bibliographic coupling. Forty-three articles, published in the journal Information Retrieval, are used as test documents. We investigate how well the approaches agree with a ground truth subject classification of the test documents, when the complete linkage method is used, and under two types of similarities, first-order and second-order. The results show that it is possible to achieve a very good approximation of the classification by means of automatic grouping of articles. One text-only method and one combination method, under second-order similarities in both cases, give rise to cluster solutions that to a large extent agree with the classification.

  • 95.
    Ahlgren, Per
    et al.
    Department of e-Resources, University Library, Stockholm University.
    Colliander, Cristian
    Umeå universitet, Samhällsvetenskapliga fakulteten, Sociologiska institutionen.
    Persson, Olle
    Umeå universitet, Samhällsvetenskapliga fakulteten, Sociologiska institutionen.
    Field normalized citation rates, field normalized journal impact and Norwegian weights for allocation of university research funds2012Ingår i: Scientometrics, ISSN 0138-9130, E-ISSN 1588-2861, Vol. 92, nr 2, s. 767-780Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We compared three different bibliometric evaluation approaches: two citationbased approaches and one based on manual classification of publishing channels into quality levels. Publication data for two universities was used, and we worked with two levels of analysis: article and department. For the article level, we investigated the predictive power of field normalized citation rates and field normalized journal impact with respect to journal level. The results for the article level show that evaluation of journals based on citation impact correlate rather well with manual classification of journals into quality levels. However, the prediction from field normalized citation rates to journal level was only marginally better than random guessing. At the department level, we studied three different indicators in the context of research fund allocation within universities and the extent to which the three indicators produce different distributions of research funds. It turned out that the three distributions of relative indicator values were very similar, which in turn yields that the corresponding distributions of hypothetical research funds would be very similar.

  • 96.
    Ahlgren, Ulf
    Umeå universitet, Medicinska fakulteten, Umeå centrum för molekylär medicin (UCMM).
    Imaging shows insulin-producing cells in diabetes2013Ingår i: TrAC. Trends in analytical chemistry, ISSN 0165-9936, E-ISSN 1879-3142, Vol. 44, s. III-IIIArtikel i tidskrift (Övrig (populärvetenskap, debatt, mm))
  • 97.
    Ahlin, Mikael
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Ranby, Felix
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Predicting Marketing Churn Using Machine Learning Models2019Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    For any organisation that engages in marketing actions there is a need to understand how people react to communication messages that are sent. Since the introduction of General Data Protection Regulation, the requirements for personal data usage have increased and people are able to effect the way their personal information is used by companies. For instance people have the possibility to unsubscribe from communication that is sent, this is called Opt-Out and can be viewed as churning from communication channels. When a customer Opt-Out the organisation loses the opportunity to send personalised marketing to that individual which in turn result in lost revenue. 

    The aim with this thesis is to investigate the Opt-Out phenomena and build a model that is able to predict the risk of losing a customer from the communication channels. The risk of losing a customer is measured as the estimated probability that a specic individual will Opt-Out in the near future. To predict future Opt-Outs the project uses machine learning algorithms on aggregated communication and customer data. Of the algorithms that were tested the best and most stable performance was achieved by an Extreme Gradient Boosting algorithm that used simulated variables. The performance of the model is best described by an AUC score of 0.71 and a lift score of 2.21, with an adjusted threshold on data two months into the future from when the model was trained. With a model that uses simulated variables the computational cost goes up. However, the increase in performance is signicant and it can be concluded that the choice to include information about specic communications is considered relevant for the outcome of the predictions. A boosted method such as the Extreme Gradient Boosting algorithm generates stable results which lead to a longer time between model retraining sessions.

  • 98.
    Ahlinder, Jon
    et al.
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Mathisen, Peter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Nilsson, Elin
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Forsman, Mats
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Andersson, Agneta
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Thelaus, Johanna
    Division of CBRN Defence and Security, FOI, Swedish Defence Research Agency, Umeå, Sweden.
    Oligotyping reveals divergent responses of predation resistant bacteria to aquatic productivity and plankton compositionManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Predation-resistance has been suggested to be a key for persistence of pathogenic bacteria in aquatic environments. Little is known about driving factors for different types of protozoa resistant bacteria (PRB). We studied if presence of PRB is linked to specific plankton taxa, the aquatic nutrient state, or predation pressure on bacteria. Nineteen freshwater systems were sampled and analyzed for PRB, plankton composition and physicochemical variables. Three PRB genera were identified; Pseudomonas, Mycobacterium and Rickettsia. Use of minimum entropy decomposition algorithm and phylogenetic analysis showed that different nodes (representing OTUs of high taxonomic resolution) matched to environmental isolates of the three genera. Links between the PRB genera and specific plankton taxa were found, but showed different relationships depending on if 18S rRNA OTU or microscopy data were used in the analysis. Mycobacterium spp. was negatively correlated to aquatic nutrient state, while Pseudomonas showed the opposite pattern. Rickettsia spp. was positively related to predation pressure on bacteria. Both Mycobacterium and Rickettsia were more abundant in systems with high eukaryotic diversity, while Pseudomonas occurred abundantly in waters with low prokaryotic diversity. The different drivers may be explained by varying ecological strategies, where Mycobacterium and Rickettsia are slow growing and have an intracellular life style, while Pseudomonas is fast growing and opportunistic. Here we give an insight to the possibilities of newly advanced methods such as sequencing and oligotyping to link potential pathogens with biomarkers. This as a tool to assist predictions of the occurrence and persistence of environmental pathogens.

  • 99.
    Ahlkvist, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Formic and Levulinic Acid from Cellulose via Heterogeneous Catalysis2014Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The chemical industry of today is under increased pressure to develop novel green materials, bio-fuels as well as sustainable chemicals for the chemical industry. Indeed, the endeavour is to move towards more eco-friendly cost efficient production processes and technologies and chemical transformation of renewables has a central role considering the future sustainable supply of chemicals and energy needed for societies. In the Nordic countries, the importance of pulping and paper industry has been particularly pronounced and the declining European demand on these products as a result of our digitalizing world has forced the industry to look at alternative sources of revenue and profitability. In this thesis, the production of levulinic and formic acid from biomass and macromolecules has been studied. Further, the optimum reaction conditions as well as the influence of the catalyst and biomass type were also discussed.

    Nordic sulphite and sulphate (Kraft) cellulose originating from two Nordic pulp mills were used as raw materials in the catalytic synthesis of green platform chemicals, levulinic and formic acids, respectively. The catalyst of choice used in this study was a macro-porous, cationic ion-exchange resin, Amberlyst 70, for which the optimal reaction conditions leading to best yields were determined. Cellulose from Nordic pulp mills were used as raw materials in the catalytic one-pot synthesis of ‘green’ levulinic and formic acid. The kinetic experiments were performed in a temperature range of 150–200 °C and an initial substrate concentration regime ranging from 0.7 to 6.0 wt %. It was concluded that the most important parameters in the one-pot hydrolysis of biomass were the reaction temperature, initial reactant concentration, acid type as well as the raw material applied. The reaction route includes dehydration of glucose to hydroxymethylfurfural as well as its further rehydration to formic and levulinic acids. The theoretical maximum yield can hardly be obtained due to formation of humins. For this system, maximum yields of 59 mol % and 68 mol % were obtained for formic and levulinic acid, respectively. The maximum yields were separately obtained in a straight-forward conversion system only containing cellulose, water and the heterogeneous catalyst. These yields were achieved at a reaction temperature of 180 °C and an initial cellulose intake of 0.7 wt % and belong to the upper range for solid catalysts so far presented in the literature.

    The reaction network of the various chemical species involved was investigated and a simple mechanistic approach involving first order reaction kinetics was developed. The concept introduces a one-pot procedure providing a feasible route to green platform chemicals obtained via conversion of coniferous soft wood pulp to levulinic and formic acids, respectively. The model was able to describe the behaviour of the system in a satisfactory manner (degree of explanation 97.8 %). Since the solid catalyst proved to exhibit good mechanical strength under the experimental conditions applied here and a one-pot procedure providing a route to green platform chemicals was developed. A simplified reaction network of the various chemical species involved was investigated and a mechanistic approach involving first order reaction kinetics was developed.

  • 100.
    Ahlkvist, Johan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ajaikumar, Samikannu
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Larsson, William
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mikkola, Jyri-Pekka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    One-pot catalytic conversion of Nordic pulp media into green platform chemicals2013Ingår i: Applied Catalysis A: General, ISSN 0926-860X, E-ISSN 1873-3875, Vol. 454, s. 21-29Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this paper, both sulphite and sulphate (Kraft) cellulose from Nordic pulp mills were used as raw materials in the catalytic one-pot synthesis of green platform chemicals, levulinic and formic acids, respectively. The catalyst of choice was a macro-porous, cationic ion-exchange resin, Amberlyst 70. The optimal reaction conditions were determined and the influence of various gas atmospheres was investigated. The maximum yields of 53% formic acid and 57% of levulinic acid were separately obtained in a straight-forward conversion system only containing cellulose, water and the heterogeneous catalyst. The concept introduces a one-pot procedure providing a feasible route to green platform chemicals obtained via conversion of coniferous soft wood pulp to levulinic and formic acids, respectively.

1234567 51 - 100 av 13322
RefereraExporteraLänk till träfflistan
Permanent länk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf