| 1. |
- Fromentin, S., et al.
(författare)
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Microbiome and metabolome features of the cardiometabolic disease spectrum
- 2022
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 28:2, s. 303-314
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Tidskriftsartikel (refereegranskat)abstract
- By studying individuals along a spectrum of cardiometabolic disease and adjusting for effects of lifestyle and medication, this investigation identifies alterations of the metabolome and microbiome from dysmetabolic conditions, such as obesity and type 2 diabetes, to ischemic heart disease. Previous microbiome and metabolome analyses exploring non-communicable diseases have paid scant attention to major confounders of study outcomes, such as common, pre-morbid and co-morbid conditions, or polypharmacy. Here, in the context of ischemic heart disease (IHD), we used a study design that recapitulates disease initiation, escalation and response to treatment over time, mirroring a longitudinal study that would otherwise be difficult to perform given the protracted nature of IHD pathogenesis. We recruited 1,241 middle-aged Europeans, including healthy individuals, individuals with dysmetabolic morbidities (obesity and type 2 diabetes) but lacking overt IHD diagnosis and individuals with IHD at three distinct clinical stages-acute coronary syndrome, chronic IHD and IHD with heart failure-and characterized their phenome, gut metagenome and serum and urine metabolome. We found that about 75% of microbiome and metabolome features that distinguish individuals with IHD from healthy individuals after adjustment for effects of medication and lifestyle are present in individuals exhibiting dysmetabolism, suggesting that major alterations of the gut microbiome and metabolome might begin long before clinical onset of IHD. We further categorized microbiome and metabolome signatures related to prodromal dysmetabolism, specific to IHD in general or to each of its three subtypes or related to escalation or de-escalation of IHD. Discriminant analysis based on specific IHD microbiome and metabolome features could better differentiate individuals with IHD from healthy individuals or metabolically matched individuals as compared to the conventional risk markers, pointing to a pathophysiological relevance of these features.
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| 2. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Abrahamsson, Thomas, 1956, et al.
(författare)
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Calibration and cross-validation of a car component using frequency response functions and a damping equalization technique
- 2014
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Ingår i: 26th International Conference on Noise and Vibration Engineering, ISMA 2014, Including the 5th International Conference on Uncertainty in Structural Dynamics, USD 2014. - 9789073802919 ; , s. 2625-2640
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Konferensbidrag (refereegranskat)abstract
- The calibration of an FE model of a car subframe is reported. In this calibration the minimum deviation between finite element model data and experimental data is searched for. The outcome of the calibrated model and cross-validation results are compared with results of testing being made on an ensemble of seemingly identical subframes. The subframe model has 250,440 degrees-of-freedom and the calibration is made for 16 uncertain model parameters. The efficiency of the calibration procedure under these conditions is reported. With model calibration being a cornerstone of the finite element validation procedure, the calibration problem is normally characterized as being a large scale optimization problem with many model parameters to solve for and with deviation metric that are nonlinear in these parameters. The calibrated parameters need to be found by iterative procedures, starting from initial estimates of parameter values. Sometimes these procedures get trapped in local deviation function minima and do not converge to the globally optimal calibration solution that is searched for. Here, a calibration formulation which gives a smooth deviation metric with a large radius of convergence to the global minimum is used. A method that utilizes damping equalization is used to avoid the mode correlation and mode pairing problem that need to be solved in various other model updating procedures. The method is combined with model reduction for increased speed and employs the Levenberg-Marquardt minimizer with randomized starts to achieve the calibration solution. The MATLAB-based open-domain software tool FEMcali has been used for calibration, validation and cross-validation.
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| 4. |
- Abrahamsson, Thomas, 1956, et al.
(författare)
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Calibration and Validation of a Car Subframe Finite Element Model Using Frequency Responses
- 2015
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Ingår i: Conference Proceedings of the Society for Experimental Mechanics Series. - Cham : Springer International Publishing. - 2191-5644 .- 2191-5652. - 9783319152516 ; 10, s. 9-22
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Konferensbidrag (refereegranskat)abstract
- A finite element model of a car front subframe has been calibrated against test data. Stepped-sine testing has been used to give frequency response function estimates on an ensemble of seemingly identical subframes. Therefore, the deviation between test data and simulation results can be compared in a meaningful way by the outcome of model calibration and cross-validation. Emphasis has been put on the preparation of the test pieces for high fidelity testing and on bettering the chances of getting a calibration outcome that provides insight into the physical processes that govern the subframe dynamics. The front subframe model has more than 200,000 degrees-of-freedom and 17 model calibration parameters. The efficiency of the calibration procedure under these conditions is reported. To achieve efficiency, a calibration with a smooth deviation metric is used together with a damping equalization method that eliminates the need for matching of experimental and analytical eigenmodes. The method is combined with surrogate model frequency response evaluation based on model reduction for increased speed. The Matlab based open-domain software tool FEMcali that employs the Levenberg-Marquardt minimizer with randomized starts has been used for calibration and an unregularized Gauss-Newton minimizer has been used in the cross-validation.
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| 5. |
- Alamidi, Daniel, et al.
(författare)
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COPD Patients Have Short Lung Magnetic Resonance T1 Relaxation Time.
- 2016
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Ingår i: COPD. - : Informa UK Limited. - 1541-2563 .- 1541-2555. ; 13:2, s. 153-159
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Tidskriftsartikel (refereegranskat)abstract
- Magnetic resonance imaging (MRI) may provide attractive biomarkers for assessment of pulmonary disease in clinical trials as it is free from ionizing radiation, minimally invasive and allows regional information. The aim of this study was to characterize lung MRI T1 relaxation time as a biomarker of chronic obstructive pulmonary disease (COPD); and specifically its relationship to smoking history, computed tomography (CT), and pulmonary function test (PFT) measurements in comparison to healthy age-matched controls. Lung T1 and inter-quartile range (IQR) of T1 maps from 24 COPD subjects and 12 healthy age-matched non-smokers were retrospectively analyzed from an institutional review board approved study. The subjects underwent PFTs and two separate MR imaging sessions at 1.5 tesla to test T1 repeatability. CT scans were performed on the COPD subjects. T1 repeatability (intraclass correlation coefficient) was 0.72 for repeated scans acquired on two visits. The lung T1 was significantly shorter (p < 0.0001) and T1 IQR was significantly larger (p = 0.0002) for the COPD subjects compared to healthy controls. Lung T1 significantly (p = 0.001) correlated with lung density assessed with CT. Strong significant correlations (p < 0.0001) between lung T1 and all PFT measurements were observed. Cigarette exposure did not correlate with lung T1 in COPD subjects. In conclusion, lung MRI T1 mapping shows potential as a repeatable, radiation free, non-invasive imaging technique in the evaluation of COPD.
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| 6. |
- Alamidi, Daniel, et al.
(författare)
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T1 Relaxation Time in Lungs of Asymptomatic Smokers.
- 2016
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- Interest in using T1 as a potential MRI biomarker of chronic obstructive pulmonary disease (COPD) has recently increased. Since tobacco smoking is the major risk factor for development of COPD, the aim for this study was to examine whether tobacco smoking, pack-years (PY), influenced T1 of the lung parenchyma in asymptomatic current smokers.
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| 7. |
- Brander, Søren, et al.
(författare)
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Biochemical evidence of both copper chelation and oxygenase activity at the histidine brace
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Lytic polysaccharide monooxygenase (LPMO) and copper binding protein CopC share a similar mononuclear copper site. This site is defined by an N-terminal histidine and a second internal histidine side chain in a configuration called the histidine brace. To understand better the determinants of reactivity, the biochemical and structural properties of a well-described cellulose-specific LPMO from Thermoascus aurantiacus (TaAA9A) is compared with that of CopC from Pseudomonas fluorescens (PfCopC) and with the LPMO-like protein Bim1 from Cryptococcus neoformans. PfCopC is not reduced by ascorbate but is a very strong Cu(II) chelator due to residues that interacts with the N-terminus. This first biochemical characterization of Bim1 shows that it is not redox active, but very sensitive to H2O2, which accelerates the release of Cu ions from the protein. TaAA9A oxidizes ascorbate at a rate similar to free copper but through a mechanism that produce fewer reactive oxygen species. These three biologically relevant examples emphasize the diversity in how the proteinaceous environment control reactivity of Cu with O2.
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| 8. |
- Edhborg, Fredrik, 1990, et al.
(författare)
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Triplet States of Cyanostar and Its Anion Complexes
- 2023
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Ingår i: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; 127:28, s. 5841-5850
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Tidskriftsartikel (refereegranskat)abstract
- The design of advanced optical materials based on triplet states requires knowledge of the triplet energies of the molecular building blocks. To this end, we report the triplet energy of cyanostar (CS) macrocycles, which are the key structure-directing units of small-molecule ionic isolation lattices (SMILES) that have emerged as programmable optical materials. Cyanostar is a cyclic pentamer of covalently linked cyanostilbene units that form π-stacked dimers when binding anions as 2:1 complexes. The triplet energies, ET, of the parent cyanostar and its 2:1 complex around PF6- are measured to be 1.96 and 2.02 eV, respectively, using phosphorescence quenching studies at room temperature. The similarity of these triplet energies suggests that anion complexation leaves the triplet energy relatively unchanged. Similar energies (2.0 and 1.98 eV, respectively) were also obtained from phosphorescence spectra of the iodinated form, I-CS, and of complexes formed with PF6- and IO4- recorded at 85 K in an organic glass. Thus, measures of the triplet energies likely reflect geometries close to those of the ground state either directly by triplet energy transfer to the ground state or indirectly by using frozen media to inhibit relaxation. Density functional theory (DFT) and time-dependent DFT were undertaken on a cyanostar analogue, CSH, to examine the triplet state. The triplet excitation localizes on a single olefin whether in the single cyanostar or its π-stacked dimer. Restriction of the geometrical changes by forming either a dimer of macrocycles, (CSH)2, or a complex, (CSH)2·PF6-, reduces the relaxation resulting in an adiabatic energy of the triplet state of 2.0 eV. This structural constraint is also expected for solid-state SMILES materials. The obtained T1 energy of 2.0 eV is a key guide line for the design of SMILES materials for the manipulation of triplet excitons by triplet state engineering in the future.
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| 9. |
- Forslund, Sofia K., et al.
(författare)
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Combinatorial, additive and dose-dependent drug–microbiome associations
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 600:7889, s. 500-505
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Tidskriftsartikel (refereegranskat)abstract
- During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1–5. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug–host–microbiome interactions in cardiometabolic disease.
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| 10. |
- Anasontzis, George E, 1980, et al.
(författare)
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Rice straw hydrolysis using secretomes from novel fungal isolates from Vietnam
- 2017
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Ingår i: Biomass and Bioenergy. - : Elsevier BV. - 1873-2909 .- 0961-9534. ; 99, s. 11-20
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Tidskriftsartikel (refereegranskat)abstract
- With a production of 39 million metric tons each year, rice is one of the main agricultural products of Vietnam. Thus, rice straw is a significant by-product, whose use in a biorefinery process would contribute to the bio-based transformation of the Vietnamese and South East Asian economy. In order to find novel efficient enzyme mixtures for the hydrolysis of rice straw and other agricultural residues, we took advantage of the rapidly evolving biodiversity of Vietnam and screened 1100 new fungal isolates from soil and decaying plant tissues for their CMCase activity. We selected 36 strains and evaluated them for their cellulases, xylanases, and accessory enzymes activities. Most of these isolates belonged to the genera Aspergillus and Trichoderma. We identified a few promising isolates, such as A. brunneoviolaceus FEC 156, A. niger FEC 130 and FEC 705, and A. tubingensis FEC 98, FEC 110 and FEC 644, whose produced enzyme mixtures released a mass fraction of the sugar content of alkali-treated rice straw higher than 20%, compared to 10% for Trichoderma reesei RUT C-30. We verified that the black Aspergilli are particularly efficient in their saccharification ability. We also identified strains that although they produced low amounts of cellulases and xylanases, their enzyme mixtures had high saccharification efficiencies, indicating the importance of the synergy effect, rather than the amount of enzymes available. Our results highlight the intra-species variation, especially in the Trichoderma genus, regarding the biomass degradation characteristics and the associated range of enzymatic activities.
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