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| 2. |
- Schmidt, Linnéa, et al.
(författare)
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Case-specific potentiation of glioblastoma drugs by pterostilbene
- 2016
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Ingår i: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 7:45, s. 73200-73215
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Tidskriftsartikel (refereegranskat)abstract
- Glioblastoma multiforme (GBM, astrocytoma grade IV) is the most common malignant primary brain tumor in adults. Addressing the shortage of effective treatment options for this cancer, we explored repurposing of existing drugs into combinations with potent activity against GBM cells. We report that the phytoalexin pterostilbene is a potentiator of two drugs with previously reported anti-GBM activity, the EGFR inhibitor gefitinib and the antidepressant sertraline. Combinations of either of these two compounds with pterostilbene suppress cell growth, viability, sphere formation and inhibit migration in tumor GBM cell (GC) cultures. The potentiating effect of pterostilbene was observed to a varying degree across a panel of 41 patient-derived GCs, and correlated in a case specific manner with the presence of missense mutation of EGFR and PIK3CA and a focal deletion of the chromosomal region 1p32. We identify pterostilbene-induced cell cycle arrest, synergistic inhibition of MAPK activity and induction of Thioredoxin interacting protein (TXNIP) as possible mechanisms behind pterostilbene's effect. Our results highlight a nontoxic stilbenoid compound as a modulator of anticancer drug response, and indicate that pterostilbene might be used to modulate two anticancer compounds in well-defined sets of GBM patients.
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| 3. |
- Sintorn, Ida-Maria, et al.
(författare)
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Segmentation of individual pores in 3D paper images
- 2005
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Ingår i: Nordic Pulp & Paper Research Journal. - 0283-2631. ; 20:3, s. 316-319
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we show that the void space in 3D images of paper can be successfully divided into subspaces using digital volume image analysis. The subspaces are denoted pores, which are connected to each other by contractions or narrowings, throats. This division of the void space into individual pores opens the possibility of extracting geometrical features as well as localising where pores with a certain feature are located in the paper. The method is illustrated on a 3D reconstruction from 2D Scanning Electron Microscopy images of a five layered duplex board. Examples of easily extracted features for the segmented pores and plots for some pore features versus the position in the paper are presented.
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| 4. |
- Svensson, Lennart, 1980-, et al.
(författare)
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Rigid template registration in MET images using CUDA
- 2012
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Ingår i: VISAPP 2012. - Rome : SciTePress. - 9789898565037 ; 2, s. 418-422
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Konferensbidrag (refereegranskat)abstract
- Rigid registration is a basic tool in many applications, especially in Molecular Electron Tomography (MET), and also in, e.g., registration of rigid implants in medical images and as initialization for deformable registration. As MET volumes have a low signal to noise ratio, a complete search of the six-dimensional (6D) parameter space is often employed. In this paper, we describe how rigid registration with normalized cross-correlation can be implemented on the GPU using NVIDIA's parallel computing architecture CUDA. We compare the performance to the Colores software and two Matlab implementations, one of which is using the GPU accelerated JACKET library. With well-aligned padding and using CUDA, the performance increases by an order of a magnitude, making it feasible to work with three-dimensional fitness landscapes, here denoted scoring volumes, that are generated on the fly. This will eventually enable the biologists to interactively register macromolecule chains in MET volumes piece by piece.
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| 5. |
- Tammela, Petter, et al.
(författare)
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Asymmetric supercapacitors based on carbon nanofibre and polypyrrole/nanocellulose composite electrodes
- 2015
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Ingår i: RSC Advances. - 2046-2069. ; 5:21, s. 16405-16413
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Tidskriftsartikel (refereegranskat)abstract
- Asymmetric, all-organic supercapacitors (containing an aqueous electrolyte), exhibiting a capacitance of 25 F g-1 (or 2.3 F cm-2) at a current density of 20 mA cm-2 and a maximum cell voltage of 1.6 V, are presented. The devices contain a composite consisting of polypyrrole covered Cladophora cellulose fibres (PPy-cellulose) as the positive electrode while a carbon nanofibre material, obtained by heat treatment of the same PPy-cellulose composite under nitrogen gas flow, serves as the negative electrode. Scanning and transmission electron microscopy combined with X-ray photoelectron spectroscopy data show that the heat treatment gives rise to a porous carbon nanofibre material, topologically almost identical to the original PPy-cellulose composite. The specific gravimetric capacitances of the carbon and the PPy-cellulose electrodes were found to be 59 and 146 F g-1, respectively, while the asymmetric supercapacitors exhibited a gravimetric energy density of 33 J g-1. The latter value is about two times higher than the energy densities obtainable for a symmetric PPy-cellulose device as a result of the larger cell voltage range accessible. The capacitance obtained for the asymmetric devices at a current density of 156 mA cm-2 was 11 F g-1 and cycling stability results further indicate that the capacity loss was about 23% during 1000 cycles employing a current density of 20 mA cm-2. The present results represent a significant step forward towards the realization of all-organic material based supercapacitors with aqueous electrolytes and commercially viable capacitances and energy densities.
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| 6. |
- Adler, Jeremy, et al.
(författare)
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Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous.
- 2019
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- Cells are neither flat nor smooth, which has serious implications for prevailing plasma membrane models and cellular processes like cell signalling, adhesion and molecular clustering. Using probability distributions from diffusion simulations, we demonstrate that 2D and 3D Euclidean distance measurements substantially underestimate diffusion on non-flat surfaces. Intuitively, the shortest within surface distance (SWSD), the geodesic distance, should reduce this problem. The SWSD is accurate for foldable surfaces but, although it outperforms 2D and 3D Euclidean measurements, it still underestimates movement on deformed surfaces. We demonstrate that the reason behind the underestimation is that topographical features themselves can produce both super- and subdiffusion, i.e. the appearance of anomalous diffusion. Differentiating between topography-induced and genuine anomalous diffusion requires characterising the surface by simulating Brownian motion on high-resolution cell surface images and a comparison with the experimental data.
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| 7. |
- Allalou, Amin, 1981-
(författare)
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Methods for 2D and 3D Quantitative Microscopy of Biological Samples
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- New microscopy techniques are continuously developed, resulting in more rapid acquisition of large amounts of data. Manual analysis of such data is extremely time-consuming and many features are difficult to quantify without the aid of a computer. But with automated image analysis biologists can extract quantitative measurements and increases throughput significantly, which becomes particularly important in high-throughput screening (HTS). This thesis addresses automation of traditional analysis of cell data as well as automation of both image capture and analysis in zebrafish high-throughput screening. It is common in microscopy images to stain the nuclei in the cells, and to label the DNA and proteins in different ways. Padlock-probing and proximity ligation are highly specific detection methods that produce point-like signals within the cells. Accurate signal detection and segmentation is often a key step in analysis of these types of images. Cells in a sample will always show some degree of variation in DNA and protein expression and to quantify these variations each cell has to be analyzed individually. This thesis presents development and evaluation of single cell analysis on a range of different types of image data. In addition, we present a novel method for signal detection in three dimensions. HTS systems often use a combination of microscopy and image analysis to analyze cell-based samples. However, many diseases and biological pathways can be better studied in whole animals, particularly those that involve organ systems and multi-cellular interactions. The zebrafish is a widely-used vertebrate model of human organ function and development. Our collaborators have developed a high-throughput platform for cellular-resolution in vivo chemical and genetic screens on zebrafish larvae. This thesis presents improvements to the system, including accurate positioning of the fish which incorporates methods for detecting regions of interest, making the system fully automatic. Furthermore, the thesis describes a novel high-throughput tomography system for screening live zebrafish in both fluorescence and bright field microscopy. This 3D imaging approach combined with automatic quantification of morphological changes enables previously intractable high-throughput screening of vertebrate model organisms.
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