| 1. |
|
|
| 2. |
- Schepke, Elizabeth, et al.
(författare)
-
DNA methylation profiling improves routine diagnosis of paediatric central nervous system tumours: A prospective population-based study
- 2022
-
Ingår i: Neuropathology and Applied Neurobiology. - : Wiley. - 0305-1846 .- 1365-2990. ; 48:6
-
Tidskriftsartikel (refereegranskat)abstract
- Aims: Paediatric brain tumours are rare, and establishing a precise diagnosis can be challenging. Analysis of DNA methylation profiles has been shown to be a reliable method to classify central nervous system (CNS) tumours with high accuracy. We aimed to prospectively analyse CNS tumours diagnosed in Sweden, to assess the clinical impact of adding DNA methylation-based classification to standard paediatric brain tumour diagnostics in an unselected cohort. Methods: All CNS tumours diagnosed in children (0-18 years) during 2017-2020 were eligible for inclusion provided sufficient tumour material was available. Tumours were analysed using genome-wide DNA methylation profiling and classified by the MNP brain tumour classifier. The initial histopathological diagnosis was compared with the DNA methylation-based classification. For incongruent results, a blinded re-evaluation was performed by an experienced neuropathologist. Results: Two hundred forty tumours with a histopathology-based diagnosis were profiled. A high-confidence methylation score of 0.84 or more was reached in 78% of the cases. In 69%, the histopathological diagnosis was confirmed, and for some of these also refined, 6% were incongruent, and the re-evaluation favoured the methylation-based classification. In the remaining 3% of cases, the methylation class was non-contributory. The change in diagnosis would have had a direct impact on the clinical management in 5% of all patients. Conclusions: Integrating DNA methylation-based tumour classification into routine clinical analysis improves diagnostics and provides molecular information that is important for treatment decisions. The results from methylation profiling should be interpreted in the context of clinical and histopathological information.
|
|
| 3. |
- Allard, Erik, et al.
(författare)
-
Comparing capillary electrophoresis : mass spectrometry fingerprints of urine samples obtained after intake of coffee, tea, or water.
- 2008
-
Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 80:23, s. 8946-8955
-
Tidskriftsartikel (refereegranskat)abstract
- Metabolomic fingerprinting is a growing strategy for characterizing complex biological samples without detailed prior knowledge about the metabolic system. A two-way analysis system with liquid separation and mass spectrometric detection provides detail-rich data suitable for such fingerprints. As a model study, human urine samples, obtained after intake of coffee, tea, or water, were analyzed with capillary electrophoresis electrospray ionization time-of-flight mass spectrometry (CE−ESI-TOF-MS). In-house-developed software (in Matlab) was utilized to manage and explore the large amount of data acquired (230 CE−MS runs, each with 50−100 million nonzero data points). After baseline and noise reduction, followed by suitable binning in time and m/z, the data sets comprised 9 and 14 million data points in negative and positive ESI mode, respectively. Finally, a signal threshold was applied, further reducing the number to about 100 000 data points per data set. A set of interactive exploratory tools, utilizing principal component analysis (PCA) and analysis of variance (ANOVA) results based on a general linear model, facilitated visual interpretation with score plots (for group assessment) and differential fingerprints (for “hot spot” detection). In the model study highly significant differences due to beverage intake were obtained among the 10 first principal components (p < 10−6 for two of the components in both ESI modes). Especially, the contrasts between “coffee” and “tea or water” indicated several “hot spots” with highly elevated intensities (e.g., for uncharged masses 93, 94, 109, 119, 123, 132, 148, 169, 178, 187, 190, and 193) suitable for further analysis, for example, with tandem MS.
|
|
| 4. |
|
|
| 5. |
|
|
| 6. |
- Danielsson, Helena, et al.
(författare)
-
An ozone response relationship for four Phleum pratense genotypes based on modelling of the phytotoxic ozone dose (POD)
- 2013
-
Ingår i: Environmental and Experimental Botany. - : Elsevier BV. - 0098-8472. ; 90, s. 70-77
-
Tidskriftsartikel (refereegranskat)abstract
- In the last decade extensive research has focused on the development of dose–response relationships based on stomatal plant ozone uptake (phytotoxic ozone dose, POD). So far most work has concentrated on crops and forest trees. This study provides a flux-based dose–response function for timothy (Phleum pratense), a widespread grassland species, which can be used in risk assessment for ground-level ozone. In 1996 and 2001 timothy was exposed in open-top chambers to ozone concentrations ranging from around 10 nmol mol−1 in the charcoal filtered treatments up to 60 nmol mol−1 in the fumigated treatments (08:00–20:00) in. In 1996 there was a negative effect of ozone on biomass production in the non-filtered treatment while in 2001 no such ozone effect in the non-filtered treatment could be seen. Measurements of stomatal conductance on four timothy genotypes in 2001 were used to calibrate a Jarvis-type multiplicative stomatal conductance model. The maximum conductance varied between the genotypes, from 477 to 589 mmol O3 m−2 s−1 (projected leaf area). The model includes functions describing the reduction of stomatal conductance of senescing leaves and the direct effects on stomatal conductance by light, temperature and water vapour pressure deficit. A function describing ozone induced senescence of the leaves was included since exposure to ozone is known to cause premature senescence. The function for ozone was applied when it suggested ozone to be more limiting to stomatal conductance than phenology. To avoid overestimation of stomatal conductance in days with high VPD, a function reflecting the effect on leaf water potential on stomatal conductance was included. Comparison between modelled and measured conductance for the four timothy genotypes resulted in an r2 value at 0.57 and a very small average deviation of observed from modelled values. The calibrated stomatal conductance model was used to estimate the accumulated POD, i.e. the accumulated stomatal flux of ozone, of the plants in the 1996 and 2001 experiments. The strongest relationship between ozone relative effects on biomass was obtained when POD was accumulated from 105 degree days after emergence to 1000 degree days after emergence, and integrated using an uptake rate threshold of 7 nmol m−2 s−1 (POD7). The response relationship between biomass and POD7 resulted in an r2 value of 0.71 over all four genotypes. This r2 value was somewhat higher than for the corresponding relationship based on the accumulated ozone exposure over 40 nmol mol−1 (AOT40; r2 = 0.66). With an uptake rate threshold at 7 nmol m−2 s−1, ozone concentrations above ∼20 nmol mol−1, contribute to reduce the biomass production of timothy if meteorological conditions promote maximum stomatal conductance.
|
|
| 7. |
- Danielsson, Henrik, et al.
(författare)
-
Brittle Failure Modes in Nailed Steel Plate Connections
- 2016
-
Ingår i: World Conference on Timber Engineering 2016.
-
Konferensbidrag (refereegranskat)abstract
- This paper deals with theoretical and experimental investigations of nailed steel plate connections. For the experimental part, a total of 43 laboratory tests on connections loaded in tension parallel to the grain are reported. The paper deals also with finite element analysis of the connection, presenting a study on the 3D stress distributions within the wood member and a study of the progressive wood fracture course by the use of a 3D nonlinear fracture mechanics model, more precisely a cohesive zone model. Results of the experimental tests are compared to results of the numerical analyses and to strength predictions according to Eurocode 5. The comparison between theoretical and experimental results indicate that the Eurocode 5 design approach for plug shear failure in nailed steel plate connections might be nonconservative in relation to predicted strength values. Also failure modes predicted by Eurocode 5 are often erroneous. Results of the numerical analyses indicate that load eccentricity has a major influence on the connection strength.
|
|
| 8. |
|
|
| 9. |
- Danielsson, Per-Erik, et al.
(författare)
-
A modified fast marching method
- 2003
-
Ingår i: Image Analysis. - : Springer Berlin/Heidelberg. - 3540406018 - 9783540451037 - 9783540406013 ; , s. 1154-1161
-
Bokkapitel (refereegranskat)abstract
- In most, if not all fast marching methods published hitherto, the input,cost function and the output arrival time are sampled on exactly the same grid. But since the input data samples are differences of the output samples. we found it natural to separate the input and output grid half a sampling unit in all coordinates (two or three). We also employ 8-neighborhood (26-neighborhood in the 3D-case) in the basic updating step of the algorithm. Some simple numerical experiments verify that the modified method improves the accuracy considerably. However, we also feel the modified method leads itself more naturally to image processing applications like tracking and segmentation.
|
|
| 10. |
- Danielsson, Per-Erik, et al.
(författare)
-
A Proposal for Combining FBP and ART in CT-reconstruction
- 2003
-
Ingår i: Proceedings of the Seventh International Meeting on Fully Three-dimensional Image Reconstruction in Radiology and Nuclear Medicine, St Malo, France, June 30 - July 4, 2003.
-
Konferensbidrag (refereegranskat)abstract
- This paper presents a proposal (not entirely new) for combining analytical and algebraic reconstruction techniques. Such a combination bears the promise to improve the image quality of fast but non-exact, reconstruction of the filtered backprojection type. The difference between the present proposal and traditional ART is that we compute a full error image with FBP, applied to projection differences, to update the solution in each iteration step. The main road-block seems to be the same that has been an obstacle for many ART-algorithms in CT applications, namely that the forward projections are subjected to ailiasing, which tend to override the intended benefits of the updating loop. We present an analysis of this problem and indicate some possible solutions.
|
|
