| 1. |
- Andersson, Magnus, et al.
(författare)
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Carbonatite ring-complexes explained by caldera-style volcanism
- 2013
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Carbonatites are rare, carbonate-rich magmatic rocks that make up a minute portion of the crust only, yet they are of great relevance for our understanding of crustal and mantle processes. Although they occur in all continents and from Archaean to present, the deeper plumbing system of carbonatite ring-complexes is usually poorly constrained. Here, we show that carbonatite ring-complexes can be explained by caldera-style volcanism. Our geophysical investigation of the Alnö carbonatite ring-complex in central Sweden identifies a solidified saucer-shaped magma chamber at ∼3 km depth that links to surface exposures through a ring fault system. Caldera subsidence during final stages of activity caused carbonatite eruptions north of the main complex, providing the crucial element to connect plutonic and eruptive features of carbonatite magmatism. The way carbonatite magmas are stored, transported and erupt at the surface is thus comparable to known emplacement styles from silicic calderas.
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| 2. |
- Andersson, Magnus, et al.
(författare)
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Magma transport in sheet intrusions of the Alnö carbonatite complex, central Sweden
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Magma transport through the Earth's crust occurs dominantly via sheet intrusions, such as dykes and cone-sheets, and is fundamental to crustal evolution, volcanic eruptions and geochemical element cycling. However, reliable methods to reconstruct flow direction in solidified sheet intrusions have proved elusive. Anisotropy of magnetic susceptibility (AMS) in magmatic sheets is often interpreted as primary magma flow, but magnetic fabrics can be modified by post-emplacement processes, making interpretation of AMS data ambiguous. Here we present AMS data from cone-sheets in the Alno carbonatite complex, central Sweden. We discuss six scenarios of syn- and post-emplacement processes that can modify AMS fabrics and offer a conceptual framework for systematic interpretation of magma movements in sheet intrusions. The AMS fabrics in the Alno cone-sheets are dominantly oblate with magnetic foliations parallel to sheet orientations. These fabrics may result from primary lateral flow or from sheet closure at the terminal stage of magma transport. As the cone-sheets are discontinuous along their strike direction, sheet closure is the most probable process to explain the observed AMS fabrics. We argue that these fabrics may be common to cone-sheets and an integrated geology, petrology and AMS approach can be used to distinguish them from primary flow fabrics.
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| 3. |
- Dahlberg, Tobias, et al.
(författare)
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3D printed water-soluble scaffolds for rapid production of PDMS micro-fluidic flow chambers
- 2018
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- We report a novel method for fabrication of three-dimensional (3D) biocompatible micro-fluidic flow chambers in polydimethylsiloxane (PDMS) by 3D-printing water-soluble polyvinyl alcohol (PVA) filaments as master scaffolds. The scaffolds are first embedded in the PDMS and later residue-free dissolved in water leaving an inscription of the scaffolds in the hardened PDMS. We demonstrate the strength of our method using a regular, cheap 3D printer, and evaluate the inscription process and the channels micro-fluidic properties using image analysis and digital holographic microscopy. Furthermore, we provide a protocol that allows for direct printing on coverslips and we show that flow chambers with a channel cross section down to 40 x 300 μm can be realized within 60 min. These flow channels are perfectly transparent, biocompatible and can be used for microscopic applications without further treatment. Our proposed protocols facilitate an easy, fast and adaptable production of micro-fluidic channel designs that are cost-effective, do not require specialized training and can be used for a variety of cell and bacterial assays. To help readers reproduce our micro-fluidic devices, we provide: full preparation protocols, 3D-printing CAD files for channel scaffolds and our custom-made molding device, 3D printer build-plate leveling instructions, and G-code.
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| 4. |
- Kimanius, Dari, et al.
(författare)
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Uptake dynamics in the Lactose permease (LacY) membrane protein transporter
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The sugar transporter Lactose permease (LacY) of Escherichia coli has become a prototype to understand the underlying molecular details of membrane transport. Crystal structures have trapped the protein in sugar-bound states facing the periplasm, but with narrow openings unable to accommodate sugar. Therefore, the molecular details of sugar uptake remain elusive. In this work, we have used extended simulations and metadynamics sampling to explore a putative sugar-uptake pathway and associated free energy landscape. We found an entrance at helix-pair 2 and 11, which involved lipid head groups and residues Gln 241 and Gln 359. Furthermore, the protein displayed high flexibility on the periplasmic side of Phe 27, which is located at the narrowest section of the pathway. Interactions to Phe 27 enabled passage into the binding site, which was associated with a 24 +/- 4 kJ/mol binding free energy in excellent agreement with an independent binding free energy calculation and experimental data. Two free energy minima corresponding to the two possible binding poses of the lactose analog beta-D-galactopyranosyl-1-thio-beta-D-galactopyranoside (TDG) were aligned with the crystal structure-binding pocket. This work outlines the chemical environment of a putative periplasmic sugar pathway and paves way for understanding substrate affinity and specificity in LacY.
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| 5. |
- Lindahl, Viveca, et al.
(författare)
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Permeability and ammonia selectivity in aquaporin TIP2;1 : linking structure to function
- 2018
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Aquaporin TIP2;1 is a protein channel that is permeable to both water and ammonia. Thestructural origin of ammonia selectivity remains obscure, but experiments have revealed that adouble mutation renders it impermeable to ammonia without affecting water permeability. Here,we aim to reproduce and explain these observations by performing an extensive mutationalstudy using microsecond long molecular dynamics simulations, applying two popular force fields.We calculate permeabilities and free energy profiles along the channel axis, for ammonia andwater. For one force field, the permeability of the double mutant decreases by a factor of 2.5 forwater and a factor of 4 for ammonia, thus increasing the selectivity for water. We attribute thiseffect to decreased entropy of water in the pore, due to the observed increase in pore–waterinteractions and narrower pore. Additionally, we observe spontaneous opening and closing ofthe pore on the cytosolic side, which suggests a gating mechanism for the pore. Our resultsshow that sampling methods and simulation times are sufficient to delineate even subtle effectsof mutations on structure and function and to capture important long-timescale events, butalso underline the importance of improving models further.
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| 6. |
- Lindahl, Viveca, et al.
(författare)
-
Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
-
Ingår i: Scientific Reports. - 2045-2322.
-
Tidskriftsartikel (refereegranskat)abstract
- Aquaporin TIP2;1 is a protein channel that is permeable to both water and ammonia. Thestructural origin of ammonia selectivity remains obscure, but experiments have revealed that adouble mutation renders it impermeable to ammonia without affecting water permeability. Here,we aim to reproduce and explain these observations by performing an extensive mutationalstudy using microsecond long molecular dynamics simulations, applying two popular force fields.We calculate permeabilities and free energy profiles along the channel axis, for ammonia andwater. For one force field, the permeability of the double mutant decreases by a factor of 2.5 forwater and a factor of 4 for ammonia, thus increasing the selectivity for water. We attribute thiseffect to decreased entropy of water in the pore, due to the observed increase in pore–waterinteractions and narrower pore. Additionally, we observe spontaneous opening and closing ofthe pore on the cytosolic side, which suggests a gating mechanism for the pore. Our resultsshow that sampling methods and simulation times are sufficient to delineate even subtle effectsof mutations on structure and function and to capture important long-timescale events, butalso underline the importance of improving models further.
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| 7. |
- Mortezaei, Narges, et al.
(författare)
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P-fimbriae in the presence of anti-PapA antibodies : new insight of antibodies action against pathogens
- 2013
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Uropathogenic strains of Escherichia coli establish urinary tract infections by attaching to host epithelial cells using adhesive organelles called fimbriae. Fimbriae are helix-like structures with a remarkable adaptability, offering safeguarding for bacteria exposed to changing fluid forces in the urinary tract. We challenged this property of P-fimbriae by cross-linking their subunits with shaft-specific antibodies and measuring the corresponding force response at a single organelle level. Our data show compromised extension and rewinding of P-fimbriae in the presence of antibodies and reduced fimbrial elasticity, which are important properties of fimbriae contributing to the ability of bacteria to cause urinary tract infections. The reduced elasticity found by cross-linking fimbrial subunits could thus be another assignment for antibodies; in addition to marking bacteria as foreign, antibodies physically compromise fimbrial function. We suggest that our assay and results will be a starting point for further investigations aimed at inhibiting sustained bacterial adhesion by antibodies.
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| 8. |
- Nilsson, Daniel, et al.
(författare)
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Patient-specific brain arteries molded as a flexible phantom model using 3D printed water-soluble resin
- 2022
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Visualizing medical images from patients as physical 3D models (phantom models) have many roles in the medical field, from education to preclinical preparation and clinical research. However, current phantom models are generally generic, expensive, and time-consuming to fabricate. Thus, there is a need for a cost- and time-efficient pipeline from medical imaging to patient-specific phantom models. In this work, we present a method for creating complex 3D sacrificial molds using an off-the-shelf water-soluble resin and a low-cost desktop 3D printer. This enables us to recreate parts of the cerebral arterial tree as a full-scale phantom model (10×6×410×6×4 cm) in transparent silicone rubber (polydimethylsiloxane, PDMS) from computed tomography angiography images (CTA). We analyzed the model with magnetic resonance imaging (MRI) and compared it with the patient data. The results show good agreement and smooth surfaces for the arteries. We also evaluate our method by looking at its capability to reproduce 1 mm channels and sharp corners. We found that round shapes are well reproduced, whereas sharp features show some divergence. Our method can fabricate a patient-specific phantom model with less than 2 h of total labor time and at a low fabrication cost.
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| 9. |
- Patel, H., et al.
(författare)
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Proteomic blood profiling in mild, severe and critical COVID-19 patients
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- The recent SARS-CoV-2 pandemic manifests itself as a mild respiratory tract infection in most individuals, leading to COVID-19 disease. However, in some infected individuals, this can progress to severe pneumonia and acute respiratory distress syndrome (ARDS), leading to multi-organ failure and death. This study explores the proteomic differences between mild, severe, and critical COVID-19 positive patients to further understand the disease progression, identify proteins associated with disease severity, and identify potential therapeutic targets. Blood protein profiling was performed on 59 COVID-19 mild (n=26), severe (n=9) or critical (n=24) cases and 28 controls using the OLINK inflammation, autoimmune, cardiovascular and neurology panels. Differential expression analysis was performed within and between disease groups to generate nine different analyses. From the 368 proteins measured per individual, more than 75% were observed to be significantly perturbed in COVID-19 cases. Six proteins (IL6, CKAP4, Gal-9, IL-1ra, LILRB4 and PD-L1) were identified to be associated with disease severity. The results have been made readily available through an interactive web-based application for instant data exploration and visualization, and can be accessed at https://phidatalab-shiny.rosalind.kcl.ac.uk/COVID19/. Our results demonstrate that dynamic changes in blood proteins associated with disease severity can potentially be used as early biomarkers to monitor disease severity in COVID-19 and serve as potential therapeutic targets.
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| 10. |
- Qamar, Saqib, et al.
(författare)
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A hybrid CNN-Random Forest algorithm for bacterial spore segmentation and classification in TEM images
- 2023
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- We present a new approach to segment and classify bacterial spore layers from Transmission Electron Microscopy (TEM) images using a hybrid Convolutional Neural Network (CNN) and Random Forest (RF) classifier algorithm. This approach utilizes deep learning, with the CNN extracting features from images, and the RF classifier using those features for classification. The proposed model achieved 73% accuracy, 64% precision, 46% sensitivity, and 47% F1-score with test data. Compared to other classifiers such as AdaBoost, XGBoost, and SVM, our proposed model demonstrates greater robustness and higher generalization ability for non-linear segmentation. Our model is also able to identify spores with a damaged core as verified using TEMs of chemically exposed spores. Therefore, the proposed method will be valuable for identifying and characterizing spore features in TEM images, reducing labor-intensive work as well as human bias.
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