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1.
  • Karlsson, Magnus, 1972-, et al. (creator_code:aut_t)
  • Application of a mass-balance model to predict PCDD/F turnover in a Baltic coastal estuary
  • 2010
  • record:In_t: Estuarine, Coastal and Shelf Science. - : Elsevier BV. - 0272-7714 .- 1096-0015. ; 88:2, s. 209-218
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • A dynamical, process-based mass-balance model was applied to quantify the transports of polychlorinated-p-dibenzodioxins and dibenzofurans (PCDD/Fs) to, within and from the Kallrigafjarden Bay, a coastal estuary in the Baltic Sea, and to predict the PCDD/F levels in the water and sediments of the bay. Before the modelling, a one-year sampling programme was implemented in 2007-2008 to measure the flows of PCDD/Fs in tributaries entering the system, the fluxes from the adjacent sea and the levels in water, sediment and fish within the estuary. The collected data set was used as input data to the model and for validation purposes. The model was originally developed and tested for suspended particulate matter and phosphorus in Baltic coastal areas. In this work, it was run monthly without any tuning of the original model variables. The simulation results compared favourably with the field measurements of levels of 15 PCDD/F congeners in the water and sediments of the bay. The dominating fluxes of PCDD/Fs were the exchange with the adjacent sea, followed by riverine input, atmospheric deposition and sediment burial. Although the sediment-water exchange was of minor importance for the overall mass-balance due to the rapid water turnover and limited areas favourable for the long-term deposition of fine sedimentary matter, sensitivity analyses indicated that the model's predictive capability was improved with about 5% by taking the sediment burial and release into account.
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2.
  • Axner, Ove, et al. (creator_code:aut_t)
  • Unraveling the secrets of bacterial adhesion organelles using single-molecule force spectroscopy
  • 2010
  • record:In_t: Single molecule spectroscopy in chemistry, physics and biology. - Berlin, Heidelberg : Springer. - 9783642025969 ; , s. 337-362
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • Many types of bacterium express micrometer-long attachment organelles (so-called pili) whose role is to mediate adhesion to host tissue. Until recently, little was known about their function in the adhesion process. Force-measuring optical tweezers (FMOT) have since then been used to unravel the biomechanical properties of various types of pili, primarily those from uropathogenic E. coli, in particular their force-vs.-elongation response, but lately also some properties of the adhesin situated at the distal end of the pilus. This knowledge provides an understanding of how piliated bacteria can sustain external shear forces caused by rinsing processes, e.g., urine flow. It has been found that many types of pilus exhibit unique and complex force-vs.-elongation responses. It has been conjectured that their dissimilar properties impose significant differences in their ability to sustain external forces and that different types of pilus therefore have dissimilar predisposition to withstand different types of rinsing conditions. An understanding of these properties is of high importance since it can serve as a basis for finding new means to combat bacterial adhesion, including that caused by antibiotic-resistance bacteria. This work presents a review of the current status of the assessment of biophysical properties of individual pili on single bacteria exposed to strain/stress, primarily by the FMOT technique. It also addresses, for the first time, how the elongation and retraction properties of the rod couple to the adhesive properties of the tip adhesin.
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3.
  • Guerra, Lina, et al. (creator_code:aut_t)
  • The biology of the cytolethal distending toxins
  • 2011
  • record:In_t: Toxins. - : MDPI. - 2072-6651 .- 2072-6651. ; 3:3, s. 172-190
  • swepub:Mat_researchreview_t (swepub:level_refereed_t)abstract
    • The cytolethal distending toxins (CDTs), produced by a variety of Gram-negative pathogenic bacteria, are the first bacterial genotoxins described, since they cause DNA damage in the target cells. CDT is an A-B(2) toxin, where the CdtA and CdtC subunits are required to mediate the binding on the surface of the target cells, allowing internalization of the active CdtB subunit, which is functionally homologous to the mammalian deoxyribonuclease I. The nature of the surface receptor is still poorly characterized, however binding of CDT requires intact lipid rafts, and its internalization occurs via dynamin-dependent endocytosis. The toxin is retrograde transported through the Golgi complex and the endoplasmic reticulum, and subsequently translocated into the nuclear compartment, where it exerts the toxic activity. Cellular intoxication induces DNA damage and activation of the DNA damage responses, which results in arrest of the target cells in the G1 and/or G2 phases of the cell cycle and activation of DNA repair mechanisms. Cells that fail to repair the damage will senesce or undergo apoptosis. This review will focus on the well-characterized aspects of the CDT biology and discuss the questions that still remain unanswered.
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4.
  • Höglander, Helena, et al. (creator_code:aut_t)
  • Pelagial biologi /växtplankton
  • 2011
  • record:In_t: Havet. - Stockholm : Naturvårdsverket. - 9789162012885 - 9789163397639 - 9789187025006 ; , s. 32-33
  • swepub:Mat_chapter_t (swepub:level_scientificother_t)
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5.
  • Lindström, Anton, 1976-, et al. (creator_code:aut_t)
  • Postprocessing of docked protein-ligand complexes using implicit solvation models
  • 2011
  • record:In_t: Journal of chemical information and modeling. - : American Chemical Society (ACS). - 1549-960X .- 1549-9596. ; 51:2, s. 267-282
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification of the bioactive conformation of a protein−ligand complex and the ranking of different ligands with respect to their strength of binding to a particular target. We have investigated the effect of implicit water on the postprocessing of binding poses generated by molecular docking using MM-PB/GB-SA (molecular mechanics Poisson−Boltzmann and generalized Born surface area) methodology. The investigation was divided into three parts: geometry optimization, pose selection, and estimation of the relative binding energies of docked protein−ligand complexes. Appropriate geometry optimization afforded more accurate binding poses for 20% of the complexes investigated. The time required for this step was greatly reduced by minimizing the energy of the binding site using GB solvation models rather than minimizing the entire complex using the PB model. By optimizing the geometries of docking poses using the GBHCT+SA model then calculating their free energies of binding using the PB implicit solvent model, binding poses similar to those observed in crystal structures were obtained. Rescoring of these poses according to their calculated binding energies resulted in improved correlations with experimental binding data. These correlations could be further improved by applying the postprocessing to several of the most highly ranked poses rather than focusing exclusively on the top-scored pose. The postprocessing protocol was successfully applied to the analysis of a set of Factor Xa inhibitors and a set of glycopeptide ligands for the class II major histocompatibility complex (MHC) Aq protein. These results indicate that the protocol for the postprocessing of docked protein−ligand complexes developed in this paper may be generally useful for structure-based design in drug discovery.
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6.
  • Zhang, Hong, et al. (creator_code:aut_t)
  • The global properties of an age-dependent SI model involving pathogenic virus release and defence mechanisms for pests
  • 2010
  • record:In_t: Mathematical and computer modelling. - : Elsevier BV. - 0895-7177 .- 1872-9479. ; 52:1-2, s. 37-54
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Insect pests are common but undesirable elements in ecosystems and represent thorny problems for most developing countries. To prevent pest outbreaks, growers often resort to insect-pathogenic viruses rather than to pesticides which affect human health and the environment. The purpose of this paper is to investigate a new age-structured pest management model which describes the interaction between susceptible insect pests, infected insect pests, pathogenic viruses and defence immunity mechanisms. A feature of this model is that it accounts for the dependence of the amount of pathogenic viruses released and of the efficiency of the defence mechanisms upon the so-called age of infection. First, the asymptotic behavior of the system is established via a monotonicity argument which makes use of several integral inequalities, being shown that the infection ultimately dies out, while under certain circumstances the susceptible pests also become extinct. By means of the Michailov criterion, one then analyzes the linearized stability of the trivial equilibrium and of the semi-trivial infected pest-free equilibrium. In this regard, it is observed that the defence mechanisms and maximal length of the infective period play important roles in the dynamics of the system. Several pest controls strategies are further investigated by means of numerical simulations, which show that when the dose of pathogenic viruses released initially is larger than a certain amount the profile of the response of defence mechanisms can be modified by changing this dose. Finally, the paper is concluded with a discussion on the biological significance of the mathematical results and framework.
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7.
  • Boes, Xavier, et al. (creator_code:aut_t)
  • Evaluation of conservative lithogenic elements (Ti, Zr, Al, and Rb) to study anthropogenic element enrichments in lake sediments
  • 2011
  • record:In_t: Journal of Paleolimnology. - Dordrecht : Springer. - 0921-2728 .- 1573-0417. ; 46:1, s. 75-87
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • In lake sediment investigations of heavy metal pollution history, it has become a common approach to calculate enrichment factors (EFs) by normalizing elemental distributions to a reference lithogenic element. However, this approach requires that the reference element remains stable once it has been deposited to the sediment (it is not affected by diagenetic processes). This is rarely studied in well-controlled field experiments. Here, we test the commonly used reference elements titanium (Ti), zirconium (Zr), aluminum (Al), and rubidium (Rb). We use a unique series of freeze cores collected in different years since 1979 in Lake Nylandssjon in northern Sweden. This lake has sediment with distinct varves (annually laminated deposit). Element concentrations in individual varves were analyzed using X-ray fluorescence (XRF) spectroscopy. By tracking the newly formed surface varve from different cores across this core series, i.e., following the element concentration in a specific varve as it becomes progressively aged, it was possible to assess the potential impact of diagenetic processes on geochemical signatures. Results confirm the conservative character of the studied elements; there was neither an increasing nor a decreasing concentration trend with time during sediment ageing for any of these elements. Secondly, we addressed the question 'which of them is the most appropriate for EFs estimates with the aim of distinguishing anthropogenic from geogenic inputs, for example in pollution studies'. To assess the reliability of the EFs we used lead (Pb) as an example, because anthropogenic Pb in the sediment could be independently calculated using stable Pb isotopes. When anthropogenic Pb concentrations calculated with Pb-EFs were compared to the anthropogenic Pb concentrations derived from stable Pb isotopes, the differences found were 20% for Ti, 10% for Zr, 11% for Al, and 27% for Rb when upper continental crust concentrations were used for the background ratio. Based on the results from Nylandssjon our suggestions are that (1) when using EFs on a single core, which is the normal case in paleolimnology, multiple reference elements should be used together and (2) the results from those should be critically evaluated.
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8.
  • Marklund, Mattias, et al. (creator_code:aut_t)
  • Spin kinetic theory-quantum kinetic theory in extended phase space
  • 2010
  • record:In_t: Transport theory and statistical physics. - : Taylor & Francis. - 0041-1450 .- 1532-2424. ; 39:5-7, s. 502-523
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • The concept of phase space distribution functions and their evolution is used in the case of en enlarged phase space. In particular, we include the intrinsic spin of particles and present a quantum kinetic evolution equation for a scalar quasi-distribution function. In contrast to the proper Wigner transformation technique, for which we expect the corresponding quasi-distribution function to be a complex matrix, we introduce a spin projection operator for the density matrix in order to obtain the aforementioned scalar quasi-distribution function. There is a close correspondence between this projection operator and the Husimi (or Q) function used extensively in quantum optics. Such a function is based on a Gaussian smearing of a Wigner function, giving a positive definite distribution function. Thus, our approach gives a Wigner-Husimi quasi-distribution function in extended phase space, for which the reduced distribution function on the Bloch sphere is strictly positive. We also discuss the gauge issue and the fluid moment hierarchy based on such a quantum kinetic theory.
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9.
  • Yu, Junchun, et al. (creator_code:aut_t)
  • Thermal properties and transition studies of multi-wall carbon nanotube/nylon-6 composites
  • 2011
  • record:In_t: Carbon. - : Elsevier. - 0008-6223 .- 1873-3891. ; 49:14, s. 4858-4866
  • swepub:Mat_article_t (swepub:level_refereed_t)abstract
    • Transition behavior and thermal properties of a multi-wall carbon nanotube (MWCNT)/nylon-6 composite (P-composite) made by in situ polymerization and subsequently structurally modified by high-pressure–high-temperature treatment have been established. The thermal conductivity (κ) of nylon-6 improved 27% by the addition of 2.1 wt.% MWCNT filler simultaneously as the heat capacity per unit volume decreased 22% compared with that of nylon-6 at 1 atm and 298 K. Moreover, the MWCNT filler raises the glass transition temperature (Tg) of nylon-6, but the pressure dependence of Tg remains unchanged. A model for κ indicates that the interfacial thermal resistance between the MWCNT filler and the nylon-6 matrix decreases 20% up to 1 GPa and most significantly above 0.8 GPa. P-composite was structurally modified by a sluggish cold-crystallization transition at 1.0 GPa, 530 K, which further increased κ by as much as 37% as the crystallinity of nylon-6 improved from 31% to 58% with a preferred crystal orientation and increased crystal size.
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10.
  • Andersson, Agneta, et al. (creator_code:aut_t)
  • Hur påverkas Östersjön?
  • 2010
  • record:In_t: Sverige i nytt klimat. - Stockholm : Forskningsrådet Formas. - 9789154060405 ; , s. 117-132
  • swepub:Mat_chapter_t (swepub:level_scientificother_t)
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