| 1. |
- Hellsvik, Johan, et al.
(författare)
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General method for atomistic spin-lattice dynamics with first-principles accuracy
- 2019
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9969 .- 2469-9950. ; 99:10
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Tidskriftsartikel (refereegranskat)abstract
- We present a computationally efficient and general first-principles based method for spin-lattice simulations for solids and clusters. The method is based on a coupling of atomistic spin dynamics and molecular dynamics simulations, expressed through a spin-lattice Hamiltonian, where the bilinear magnetic term is expanded up to second order in displacement. The effect of first-order spin-lattice coupling on the magnon and phonon dispersion in bcc Fe is reported as an example, and we observe good agreement with previous simulations. We also illustrate the coupled spin-lattice dynamics method on a more conceptual level, by exploring dissipation-free spin and lattice motion of small magnetic clusters (a dimer, trimer, and tetramer). The method discussed here opens the door for a quantitative description and understanding of the microscopic origin of many fundamental phenomena of contemporary interest, such as ultrafast demagnetization, magnetocalorics, and spincaloritronics.
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| 2. |
- Memedi, Mevludin, 1983-, et al.
(författare)
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Automatic Spiral Analysis for Objective Assessment of Motor Symptoms in Parkinson's Disease
- 2015
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Ingår i: Sensors. - : MDPI AG. - 1424-8220. ; 15:9, s. 23727-23744
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Tidskriftsartikel (refereegranskat)abstract
- A challenge for the clinical management of advanced Parkinson's disease (PD) patients is the emergence of fluctuations in motor performance, which represents a significant source of disability during activities of daily living of the patients. There is a lack of objective measurement of treatment effects for in-clinic and at-home use that can provide an overview of the treatment response. The objective of this paper was to develop a method for objective quantification of advanced PD motor symptoms related to off episodes and peak dose dyskinesia, using spiral data gathered by a touch screen telemetry device. More specifically, the aim was to objectively characterize motor symptoms (bradykinesia and dyskinesia), to help in automating the process of visual interpretation of movement anomalies in spirals as rated by movement disorder specialists. Digitized upper limb movement data of 65 advanced PD patients and 10 healthy (HE) subjects were recorded as they performed spiral drawing tasks on a touch screen device in their home environment settings. Several spatiotemporal features were extracted from the time series and used as inputs to machine learning methods. The methods were validated against ratings on animated spirals scored by four movement disorder specialists who visually assessed a set of kinematic features and the motor symptom. The ability of the method to discriminate between PD patients and HE subjects and the test-retest reliability of the computed scores were also evaluated. Computed scores correlated well with mean visual ratings of individual kinematic features. The best performing classifier (Multilayer Perceptron) classified the motor symptom (bradykinesia or dyskinesia) with an accuracy of 84% and area under the receiver operating characteristics curve of 0.86 in relation to visual classifications of the raters. In addition, the method provided high discriminating power when distinguishing between PD patients and HE subjects as well as had good test-retest reliability. This study demonstrated the potential of using digital spiral analysis for objective quantification of PD-specific and/or treatment-induced motor symptoms.
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| 3. |
- Temnerud, Johan, et al.
(författare)
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Spatial patterns of some trace elements in four Swedish stream networks
- 2013
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 10, s. 1407-1423
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Tidskriftsartikel (refereegranskat)abstract
- Four river basins in southern Sweden, with catchment sizes from 0.3 to 127 km(2) (median 1.9), were sampled in October 2007. The 243 samples were analysed for 26 trace elements (Ag, As, Au, Ba, Be, Bi, Cd, Co, Cr, Cu, Ga, Ge, In, La, Li, Mo, Ni, Pb, Sb, Se, Sn, Tl, Ti, U, V and Zn) to identify spatial patterns within drainage networks. The range and median of each element were defined for different stream orders, and relationships to catchment characteristics, including deposition history, were explored. The sampling design made it possible to compare the differences along 40 stream reaches, above and below 53 stream junctions with 107 tributaries and between the 77 inlets and outlets of 36 lakes. The largest concentration differences (at reaches, junctions and lakes) were observed for lakes, with outlets usually having lower concentration compared to the inlets for As, Ba, Be, Bi, Cd, Co, Cr, Ga, Ge, Ni, Pb, Sn, Ti, Tl, U, V and Zn. Significantly lower concentrations were observed for Cd and Co when comparing headwaters with downstream sites in each catchment. Common factor analysis (FA) revealed that As, Bi, Cr, Ga, Ge, Tl and V co-vary positively with Al, Fe and total organic carbon (TOC) and negatively with La, Li and pH. The strong removal of a large number of trace elements when passing through lakes is evident though in the FA, where lake surface coverage plots opposite to many of those elements. Forest volume does not respond in a similar systematic fashion and, surprisingly, the amount of wetland does not relate strongly to either Fe or TOC at any of the rivers. A better understanding of the quantitative removal of organic carbon and iron will aid in understanding trace element fluxes from landscapes rich in organic matter and iron.
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| 4. |
- Elmabsout, Ali Ateia, et al.
(författare)
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Cloning and Functional Studies of a Splice Variant of CYP26B1 Expressed in Vascular Cells
- 2012
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Ingår i: Plos One. - San Francisco, USA : Public Library of Science (PLoS). - 1932-6203. ; 7:5
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Tidskriftsartikel (refereegranskat)abstract
- Background: All-trans retinoic acid (atRA) plays an essential role in the regulation of gene expression, cell growth and differentiation and is also important for normal cardiovascular development but may in turn be involved in cardiovascular diseases, i.e. atherosclerosis and restenosis. The cellular atRA levels are under strict control involving several cytochromes P450 isoforms (CYPs). CYP26 may be the most important regulator of atRA catabolism in vascular cells. The present study describes the molecular cloning, characterization and function of atRA-induced expression of a spliced variant of the CYP26B1 gene. Methodology/Principal Findings: The coding region of the spliced CYP26B1 lacking exon 2 was amplified from cDNA synthesized from atRA-treated human aortic smooth muscle cells and sequenced. Both the spliced variant and full length CYP26B1 was found to be expressed in cultured human endothelial and smooth muscle cells, and in normal and atherosclerotic vessel. atRA induced both variants of CYP26B1 in cultured vascular cells. Furthermore, the levels of spliced mRNA transcript were 4.5 times higher in the atherosclerotic lesion compared to normal arteries and the expression in the lesions was increased 20-fold upon atRA treatment. The spliced CYP26B1 still has the capability to degrade atRA, but at an initial rate one-third that of the corresponding full length enzyme. Transfection of COS-1 and THP-1 cells with the CYP26B1 spliced variant indicated either an increase or a decrease in the catabolism of atRA, probably depending on the expression of other atRA catabolizing enzymes in the cells. Conclusions/Significance: Vascular cells express the spliced variant of CYP26B1 lacking exon 2 and it is also increased in atherosclerotic lesions. The spliced variant displays a slower and reduced degradation of atRA as compared to the full-length enzyme. Further studies are needed, however, to clarify the substrate specificity and role of the CYP26B1 splice variant in health and disease.
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| 5. |
- Mattsson, Anna, et al.
(författare)
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Metabolic Profiling of Chicken Embryos Exposed to Perfluorooctanoic Acid ( PFOA) and Agonists to Peroxisome Proliferator-Activated Receptors
- 2015
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Ingår i: PLOS ONE. - : Public Library Science. - 1932-6203. ; 10:12
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Tidskriftsartikel (refereegranskat)abstract
- Untargeted metabolic profiling of body fluids in experimental animals and humans exposed to chemicals may reveal early signs of toxicity and indicate toxicity pathways. Avian embryos develop separately from their mothers, which gives unique possibilities to study effects of chemicals during embryo development with minimal confounding factors from the mother. In this study we explored blood plasma and allantoic fluid from chicken embryos as matrices for revealing metabolic changes caused by exposure to chemicals during embryonic development. Embryos were exposed via egg injection on day 7 to the environmental pollutant perfluorooctanoic acid (PFOA), and effects on the metabolic profile on day 12 were compared with those caused by GW7647 and rosiglitazone, which are selective agonists to peroxisome-proliferator activated receptor a (PPAR alpha) and PPAR gamma, respectively. Analysis of the metabolite concentrations from allantoic fluid by Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) showed clear separation between the embryos exposed to GW7647, rosiglitazone, and vehicle control, respectively. In blood plasma only GW7647 caused a significant effect on the metabolic profile. PFOA induced embryo mortality and increased relative liver weight at the highest dose. Sublethal doses of PFOA did not significantly affect the metabolic profile in either matrix, although single metabolites appeared to be altered. Neonatal mortality by PFOA in the mouse has been suggested to be mediated via activation of PPAR alpha. However, we found no similarity in the metabolite profile of chicken embryos exposed to PFOA with those of embryos exposed to PPAR agonists. This indicates that PFOA does not activate PPAR pathways in our model at concentrations in eggs and embryos well above those found in wild birds. The present study suggests that allantoic fluid and plasma from chicken embryos are useful and complementary matrices for exploring effects on the metabolic profile resulting from chemical exposure during embryonic development.
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| 6. |
- Chen, Deliang, 1961, et al.
(författare)
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Summary of a workshop on extreme weather events in a warming world organized by the Royal Swedish Academy of Sciences
- 2020
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Ingår i: Tellus Series B-Chemical and Physical Meteorology. - : Stockholm University Press. - 1600-0889 .- 0280-6509. ; 72:1
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Tidskriftsartikel (refereegranskat)abstract
- Climate change is not only about changes in means of climatic variables such as temperature, precipitation and wind, but also their extreme values which are of critical importance to human society and ecosystems. To inspire the Swedish climate research community and to promote assessments of international research on past and future changes in extreme weather events against the global climate change background, the Earth Science Class of the Royal Swedish Academy of Sciences organized a workshop entitled 'Extreme weather events in a warming world' in 2019. This article summarizes and synthesizes the key points from the presentations and discussions of the workshop on changes in floods, droughts, heat waves, as well as on tropical cyclones and extratropical storms. In addition to reviewing past achievements in these research fields and identifying research gaps with a focus on Sweden, future challenges and opportunities for the Swedish climate research community are highlighted.
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| 7. |
- Sjöberg, Susanne, et al.
(författare)
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Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden : impact on metal mobility
- 2020
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press. - 0168-6496 .- 1574-6941. ; 96:11
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Tidskriftsartikel (refereegranskat)abstract
- Microbe-mediated precipitation of Mn-oxides enriched in rare earth elements (REE) and other trace elements was discovered in tunnels leading to the main shaft of the Ytterby mine, Sweden. Defining the spatial distribution of microorganisms and elements in this ecosystem provide a better understanding of specific niches and parameters driving the emergence of these communities and associated mineral precipitates. Along with elemental analyses, high-throughput sequencing of the following four subsystems were conducted: (1) water seeping from a rock fracture into the tunnel, (2) Mn-oxides and associated biofilm; referred to as the Ytterby Black Substance (YBS) biofilm (3) biofilm forming bubbles on the Mn-oxides; referred to as the bubble biofilm, and (4) fracture water that has passed through the biofilms. Each subsystem hosts a specific collection of microorganisms. Differentially abundant bacteria in the YBS biofilm were identified within the Rhizobiales (e.g. Pedomicrobium), PLTA13 Gammaproteobacteria, Pirellulaceae, Hyphomonadaceae, Blastocatellia and Nitrospira. These taxa, likely driving the Mn-oxide production, were not detected in the fracture water. This biofilm binds Mn, REE and other trace elements in an efficient, dynamic process, as indicated by substantial depletion of these metals from the fracture water as it passes through the Mn deposit zone. Microbe-mediated oxidation of Mn(II) and formation of Mn(III/IV)-oxides can thus have considerable local environmental impact by removing metals from aquatic environments.
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| 8. |
- Caporale, N., et al.
(författare)
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From cohorts to molecules: Adverse impacts of endocrine disrupting mixtures
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375:6582
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Tidskriftsartikel (refereegranskat)abstract
- Convergent evidence associates exposure to endocrine disrupting chemicals (EDCs) with major human diseases, even at regulation-compliant concentrations. This might be because humans are exposed to EDC mixtures, whereas chemical regulation is based on a risk assessment of individual compounds. Here, we developed a mixture-centered risk assessment strategy that integrates epidemiological and experimental evidence. We identified that exposure to an EDC mixture in early pregnancy is associated with language delay in offspring. At human-relevant concentrations, this mixture disrupted hormone-regulated and disease-relevant regulatory networks in human brain organoids and in the model organisms Xenopus leavis and Danio rerio, as well as behavioral responses. Reinterrogating epidemiological data, we found that up to 54% of the children had prenatal exposures above experimentally derived levels of concern, reaching, for the upper decile compared with the lowest decile of exposure, a 3.3 times higher risk of language delay. © 2022 American Association for the Advancement of Science. All rights reserved.
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| 9. |
- Lindh, Ingrid, et al.
(författare)
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Production of the p24 capsid protein from HIV-1 subtype C in Arabidopsis thaliana and Daucus carota using an endoplasmic reticulum-directing SEKDEL sequence in protein expression constructs
- 2009
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Ingår i: Protein Expression and Purification. - St. Louis : Academic Press. - 1046-5928 .- 1096-0279. ; 66:1, s. 46-51
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Tidskriftsartikel (refereegranskat)abstract
- An optimized gene expression construct was designed in order to increase the accumulation of the HIV-1 subtype C p24 protein in Arabidopsis thaliana and carrot (Daucus carota) plants. An ER retention signal was introduced into the genetic construct generating a p24 protein containing a SEKDEL amino acid sequence at its C-terminus. Mature A. thaliana plants and carrot cells were transformed using Agrobacterium tumefaciens carrying the improved pGreen0229/p24_SEKDEL vector. Several transgenic plant lines were obtained from both plant species by growth on selective medium and confirmed by PCR. Transformed lines were analyzed for p24 protein content by western blotting using anti-p24-specific antibodies and by Southern blotting to establish the number of copies of the insert in the plant nuclear genome. To estimate the accumulation levels of p24 protein in the plants, ELISA was run using soluble plant extracts. By comparing these results with our previous findings, the ER retention signal increased the level of p24 protein 5-fold in the Arabidopsis thaliana plants. In carrot taproot, the content of p24_SEKDEL protein was approximately half of that in Arabidopsis on a fresh weight basis and was stable in planta for several months. However, on a total soluble protein basis, carrots produced considerable higher levels of the p24_SEKDEL protein than Arabidopsis.
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| 10. |
- Norinder, Ulf, 1956-, et al.
(författare)
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Representing descriptors derived from multiple conformations as uncertain features for machine learning
- 2013
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Ingår i: Journal of Molecular Modeling. - : Springer. - 1610-2940 .- 0948-5023. ; 19:6, s. 2679-2685
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Tidskriftsartikel (refereegranskat)abstract
- Uncertainty was introduced into the chemical descriptors of 11 datasets by conformational analysis in order to incorporate three-dimensional information and to investigate the resulting predictive performance of a state-of-the-art machine learning method, random forests, for binary classification tasks. A number of strategies for handling uncertainty in random forests were evaluated. The study showed that when incorporating three-dimensional information as uncertainty into chemical descriptors, the use of uniform probability distributions over the range of possible values, in conjunction with fractional distribution of compounds clearly outperforms the use of normal distributions as well as sampling from both normal and uniform distributions. The main conclusion of this study is that, even when distributions of uncertain values are provided, the random forest method can generate models that are almost as accurate from the expected values of these distributions alone. Hence, there seems to be little advantage to using the more elaborate methods of incorporating uncertainty in chemical descriptors when using random forests rather than replacing the distributions with single-point values. The results also show that random forest models with similar performances can also be generated using three-dimensional descriptor information derived from single (lowest-energy or Corina-derived) conformations.
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