| 1. |
- Nordin, Matias, 1981, et al.
(author)
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Estimation of mass thickness response of embedded aggregated silica nanospheres from high angle annular dark-field scanning transmission electron micrographs
- 2014
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In: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 253:2, s. 166-170
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Journal article (peer-reviewed)abstract
- In this study, we investigate the functional behaviour of the intensity in high-angle annular dark field scanning transmission electron micrograph images. The model material is a silica particle (20 nm) gel at 5 wt%. By assuming that the intensity response is monotonically increasing with increasing mass thickness of silica, an estimate of the functional form is calculated using a maximum likelihood approach. We conclude that a linear functional form of the intensity provides a fair estimate but that a power function is significantly better for estimating the amount of silica in the z-direction. The work adds to the development of quantifying material properties from electron micrographs, especially in the field of tomography methods and three-dimensional quantitative structural characterization from a scanning transmission electron micrograph. It also provides means for direct three-dimensional quantitative structural characterization from a scanning transmission electron micrograph.
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| 2. |
- Röding, Magnus, 1984, et al.
(author)
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The gamma distribution model for pulsed-field gradient NMR studies of molecular-weight distributions of polymers
- 2012
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In: Journal of Magnetic Resonance. - : Elsevier BV. - 1090-7807 .- 1096-0856. ; 222, s. 105-111
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Journal article (peer-reviewed)abstract
- Self-diffusion in polymer solutions studied with pulsed-field gradient nuclear magnetic resonance (PFG NMR) is typically based either on a single self-diffusion coefficient, or a log-normal distribution of self-diffusion coefficients, or in some cases mixtures of these. Experimental data on polyethylene glycol (PEG) solutions and simulations were used to compare a model based on a gamma distribution of self-diffusion coefficients to more established models such as the single exponential, the stretched exponential, and the log-normal distribution model with regard to performance and consistency. Even though the gamma distribution is very similar to the log-normal distribution, its NMR signal attenuation can be written in a closed form and therefore opens up for increased computational speed. Estimates of the mean self-diffusion coefficient, the spread, and the polydispersity index that were obtained using the gamma model were in excellent agreement with estimates obtained using the log-normal model. Furthermore, we demonstrate that the gamma distribution is by far superior to the log-normal, and comparable to the two other models, in terms of computational speed. This effect is particularly striking for multi-component signal attenuation. Additionally, the gamma distribution as well as the log-normal distribution incorporates explicitly a physically plausible model for polydispersity and spread, in contrast to the single exponential and the stretched exponential. Therefore, the gamma distribution model should be preferred in many experimental situations.
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| 3. |
- Steglich, Thomas, 1983, et al.
(author)
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Microstructure and water distribution of commercial pasta studied by microscopy and 3D magnetic resonance imaging
- 2014
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In: Food Research International. - : Elsevier BV. - 0963-9969 .- 1873-7145. ; 62, s. 644-652
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Journal article (peer-reviewed)abstract
- Manufacturing pasta is a rather well known process, but it is still challenging to tailor pasta products with new raw materials. In this study, we evaluated the effects of raw materials on the microstructure and water distribution in cooked pasta using H-1 magnetic resonance imaging (MRI) as well as bright field and polarized light microscopy. The MRI parameters initial intensity (I-0) and transverse dephasing time (T-2*) serve as indicators of the local water concentration and water-macromolecule interactions through chemical exchange, respectively. These parameters were mapped throughout the whole pasta volume with a spatial resolution of 78 mu m in all three dimensions. MRI was combined with light microscopy to link I-0 and T-2* to microstructure components such as fiber particles and the extent of starch gelatinization. Four commercial spaghetti samples were analyzed which were made of durum wheat flour, both plain and enriched with wheat fiber, as well as with wholegrain and soft wheat flour. Although all pasta samples showed similar macroscopic water absorption as measured by weight increase, the sample structures differed at the microscopic scale. Compared to durum wheat spaghetti, the presence of fiber particles decreased T-2*, while spaghetti enriched with soft wheat flour increased T-2*. In addition, light microscopy showed that large fiber particles partly acted as barriers against water migration and protected starch granules from swelling. Smaller wheat fiber particles did not affect local starch swelling. Thus, the combination of light microscopy and MRI is a powerful tool to study the microstructure and water distribution in pasta.
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| 4. |
- Bernin, Diana, 1979, et al.
(author)
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Multi-scale characterization of pasta during cooking using microscopy and real-time magnetic resonance imaging
- 2014
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In: Food Research International. - : Elsevier BV. - 0963-9969 .- 1873-7145. ; 66, s. 132-139
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Journal article (peer-reviewed)abstract
- Macroscopic properties of pasta, such as the texture, are formed during cooking by a complex interplay of water and heat with the structuring agents starch and gluten. The impact of the starch-to-gluten ratio on microstructure and water distribution in pasta was analyzed by a multi-scale approach combining magnetic resonance imaging (MRI) and light microscopy. The cooking process and thus the water distribution was monitored non-invasively using 1H MRI in real-time with a temporal resolution of 45s. Our MRI set-up allowed following the water ingress by imaging the reduction of the uncooked core. The water ingress rate was neither dependent on pasta composition nor on the presence of salt in the cooking media (0.7% NaCl). Starch-rich samples showed a more homogeneous water distribution in the gelatinized zone, which was mirrored in a more homogeneous microstructure. In contrast, gluten-rich samples showed both a heterogeneous water distribution and microstructure. Thus, the gluten content affected local water content in the gelatinized zone but not the water ingress. © 2014 Elsevier Ltd.
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| 5. |
- Deschout, H., et al.
(author)
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Disposable microfluidic chip with integrated light sheet illumination enables diagnostics based on membrane vesicles
- 2014
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In: 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; Freiburg; Germany; 27 October 2013 through 31 October 2013. - 9781632666246
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Conference paper (peer-reviewed)abstract
- Cell-derived membrane vesicles that are released in body fluids are emerging as potential non-invasive biomarkers for diseases like cancer. Techniques capable of measuring the size and concentration of such membrane vesicles directly in body fluids are urgently needed. Here we report on a microfluidic chip with integrated light sheet illumination, and demonstrate accurate fluorescence Single Particle Tracking measurements of the size and concentration of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours.
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| 6. |
- Deschout, Hendrik, et al.
(author)
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Disposable microfluidic chip with integrated light sheet illumination enables diagnostics based on membrane vesicles
- 2013
-
In: 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; Freiburg; Germany; 27 October 2013 through 31 October 2013. ; 3, s. 2010-2012
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Conference paper (peer-reviewed)abstract
- Cell-derived membrane vesicles that are released in body fluids are emerging as potential non-invasive biomarkers for diseases like cancer. Techniques capable of measuring the size and concentration of such membrane vesicles directly in body fluids are urgently needed. Here we report on a microfluidic chip with integrated light sheet illumination, and demonstrate accurate fluorescence Single Particle Tracking measurements of the size and concentration of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours.
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| 7. |
- Deschout, H., et al.
(author)
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On-chip light sheet illumination enables diagnostic size and concentration measurements of membrane vesicles in biofluids
- 2014
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In: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 6:3, s. 1741-1747
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Journal article (peer-reviewed)abstract
- Cell-derived membrane vesicles that are released in biofluids, like blood or saliva, are emerging as potential non-invasive biomarkers for diseases, such as cancer. Techniques capable of measuring the size and concentration of membrane vesicles directly in biofluids are urgently needed. Fluorescence single particle tracking microscopy has the potential of doing exactly that by labelling the membrane vesicles with a fluorescent label and analysing their Brownian motion in the biofluid. However, an unbound dye in the biofluid can cause high background intensity that strongly biases the fluorescence single particle tracking size and concentration measurements. While such background intensity can be avoided with light sheet illumination, current set-ups require specialty sample holders that are not compatible with high-throughput diagnostics. Here, a microfluidic chip with integrated light sheet illumination is reported, and accurate fluorescence single particle tracking size and concentration measurements of membrane vesicles in cell culture medium and in interstitial fluid collected from primary human breast tumours are demonstrated.
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| 8. |
- Naeye, B, et al.
(author)
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Hemocompatibility of siRNA loaded dextran nanogels
- 2011
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In: Biomaterials. - : Elsevier BV. - 0142-9612 .- 1878-5905. ; 32:34, s. 9120-9127
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Journal article (peer-reviewed)abstract
- Although the behavior of nanoscopic delivery systems in blood is an important parameter when contemplating their intravenous injection, this aspect is often poorly investigated when advancing from in vitro to in vivo experiments. In this paper, the behavior of siRNA loaded dextran nanogels in human plasma and blood is examined using fluorescence fluctuation spectroscopy, platelet aggregometry, flow cytometry and single particle tracking. Our results show that, in contrast to their negatively charged counterparts, positively charged siRNA loaded dextran nanogels cause platelet aggregation and show increased binding to human blood cells. Although PEGylating the nanogels did not have a significant effect on their interaction with blood cells, single particle tracking revealed that it is necessary to prevent their aggregation in human plasma. We therefore conclude that PEGylated negatively charged dextran nanogels are the most suited for further in vivo studies as they do not aggregate in human plasma and exhibit minimal interactions with blood cells.
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| 9. |
- Röding, Magnus, 1984, et al.
(author)
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Automatic Particle Detection in Microscopy Using Temporal Correlations
- 2013
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In: Microscopy Research and Technique. - : Wiley. - 1059-910X. ; 76:10, s. 997-1006
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Journal article (peer-reviewed)abstract
- One of the fundamental problems in the analysis of single particle tracking data is the detection of individual particle positions from microscopy images. Distinguishing true particles from noise with a minimum of false positives and false negatives is an important step that will have substantial impact on all further analysis of the data. A common approach is to obtain a plausible set of particles from a larger set of candidate particles by filtering using manually selected threshold values for intensity, size, shape, and other parameters describing a particle. This introduces subjectivity into the analysis and hinders reproducibility. In this paper, we introduce a method for automatic selection of these threshold values based on maximizing temporal correlations in particle count time series. We use Markov Chain Monte Carlo to find the threshold values corresponding to the maximum correlation, and we study several experimental data sets to assess the performance of the method in practice by comparing manually selected threshold values from several independent experts with automatically selected threshold values. We conclude that the method produces useful results, reducing subjectivity and the need for manual intervention, a great benefit being its easy integratability into many already existing particle detection algorithms.
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| 10. |
- Röding, Magnus, 1984
(author)
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Concentration measurements in single particle microscopy
- 2011
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Licentiate thesis (other academic/artistic)abstract
- The topic of this thesis is the introduction of two novel methods for using single particle microscopy as a tool for absolute number concentration measurements of Brownian particles. The key idea of both methods is that in order to estimate number concentration, the size of the (three-dimensional) particle detection region has to be estimated. Typically, this size has until now been estimated by means of a separate a priori calibration measurement. Thus, in many cases the influence of for example particle brightness and image analysis settings on the final result have been ignored. In the first paper, we use single particle tracking to estimate the size of the detection region. This is based on modeling the distribution of trajectory lengths within the detection region. The modeling is simplified by assuming that particles enter and exit the detection region only by means of axial diffusion, i.e. parallel to the optical axis and orthogonal to the focal plane. In the second paper, we study a time series of particle counts known as a Smoluchowski process. We approximate this non-Markov process by a Markov chain and demonstrate that this model can be used to estimate the size of the detection region. This implies that individual particles need not be tracked. We also introduce a method for automatic selection of a threshold for minimum contrast between particles and the image background, based on analyzing the correlations between particle counts in consecutive frames. In both cases, we perform experimental validation by estimation of the number concentration of different dilutions of a nanosphere water dispersion, and we find close agreement with validation measurements.
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