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- Andersson, Jan O., et al.
(författare)
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A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution
- 2007
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 8, s. 51-
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Forskningsöversikt (refereegranskat)abstract
- Background: Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus). Results: The analyses revealed a compact genome with few, if any, introns and very short 3′ untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes - mostly encoding metabolic proteins - that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals. Conclusion: Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution.
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- Berglin, Niklas, et al.
(författare)
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Pilot-scale combustion studies with kraft lignin in a powder burner and a CFB boiler
- 2010
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Ingår i: TAPPI Journal. - 0734-1415. ; 9:6, s. 24-30
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Tidskriftsartikel (refereegranskat)abstract
- Processes have been developed to produce a solid biofuel with high energy density and low ash content from kraft lignin precipitated from black liquor. Pilot-scale tests of the lignin biofuel were carried out with a 150 kW powder burner and a 12 MW circulating fluidized bed (CFB) boiler. Lignin powder could be fired in a powder burner with good combustion performance after some trimming of the air flows to reduce swirl. Lignin dried to 10% moisture content was easy to feed smoothly and had less bridging tendencies in the feeding system than did wood/ bark powder. In the CFB boiler, lignin was easily handled and cofired together with bark. Although the filter cake was broken into smaller pieces and fines, the combustion was not disturbed. When cof ¡ring lignin with bark, the sulfur emission increased compared with bark firing only, but most of the sulfur was captured by calcium in the bark ash. Conventional sulfur capture also occurred with addition of limestone to the bed. The sulfur content in the lignin had a significantly positive effect on reducing the alkali chloride content in the deposits, thus reducing the high temperature corrosion risk. Application: This research is of interest for pulp and paper and energy and utilities companies that want to understand how kraft lignin can be used to replace fuel oil or coal in many combustion applications.
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- Branger, Erik, 1988-, et al.
(författare)
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Image analysis as a tool for improved use of the Digital Cherenkov Viewing Device for inspection of irradiated PWR fuel assemblies.
- 2014
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The Digital Cherenkov Viewing Device (DCVD) is a tool used to measure the Cherenkov light emitted from irradiated nuclear fuel assemblies stored in water pools. It has been approved by the IAEA for attended gross defect verification, as well as for partial defect verification, where a fraction of the fuel material has been diverted. In this report, we have investigated the current procedures for recording images with the DCVD, and have looked into ways to improve these procedures. Using three different image sets of PWR fuel assemblies, we have analysed what information and results can be obtained using image analysis techniques. We have investigated several error sources that distort the images, and have shown how these errors affect the images. We have also described some of the errors mathematically, and have discussed how these error sources may be compensated for, if the character and magnitude of the errors are known. Resulting from our investigations are a few suggestions on how to improve the procedures and consequently the quality of the images recorded with the DCVD as well as suggestions on how to improve the analysis of collected images. Specifically, a few improvements that should be looked into in the short term are:• Images should be recorded with the fuel assembly perfectly centered in the image, and preferably without any tilt of the DCVD relative to the fuel in order to obtain accurate measurements of the light intensity. Image analysis procedures that may aid the alignment are presented.• To compensate for the distorting effect of the water surface and possible turbulence in the water, several images with short exposure time should be captured rather than one image with long exposure time. Using image analysis procedures, it is possible to sum the images resulting in a final image with less distortions and improved quality.• A reference image should be used to estimate device-related distortions, so that these distortions are compensated for. Ideally, this procedure can also be used to calibrate individual pixels.• The background should be carefully taken into account in order to separate the background level from diffuse signal components, allowing for the background to be subtracted. Accordingly, each measurement campaign should be accompanied by at least one background measurement, recorded from a section in the storage pool where no fuel assemblies are present. Furthermore, the background level should be determined from a larger region in the image and not from one individual pixel, as is currently done.• A database of measurements should be set up, containing DCVD images, information about the applied DCVD settings and the conditions that the DCVD was used in. Any partial defect verification procedure at any time could then be tested against as much data as possible. Accordingly, a database can aid in evaluating and improving partial defect verification methods using DCVD image analysis.Based on the findings and discussions in this report, some long-term improvements are also suggested.
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- Branger, Erik, 1988-, et al.
(författare)
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Improved DCVD assessments of irradiated nuclear fuel using image analysis techniques
- 2014
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The Digital Cherenkov Viewing Device (DCVD) is a tool for measuring the Cherenkov light intensity emitted from irradiated nuclear fuel in wet storage. It is currently used in nuclear facilities where authority inspectors perform attended gross defect verification to ensure the presence of irradiated fuel material, as well as partial defect verification to ensure that a fraction of the fuel material has not been diverted. In 2013, Uppsala University (UU), supported by the Swedish Radiation Safety Authority, initiated a PhD project aimed at gaining a better understanding of the underlying physics process of the Cherenkov light emission and its detection, in order to improve and enhance the capabilities of the DCVD. The scope of this research is broad and includes modelling, simulations and experiments. As a first step, expertise on image analysis was brought into the project with the purpose to identify image analysis related opportunities and challenges relevant to the DCVD. The investigations performed so far cover general aspects of image analysis as well as aspects specific for verification of PWR fuels, where the fuel geometry may be extra challenging. Resulting from the investigation are suggestions on how to improve the measurement procedure and consequently the image quality obtained with the DCVD. This presentation describes these results and expected outcomes of their implementation.
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| 6. |
- Branger, Erik, 1988-, et al.
(författare)
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Towards unattended partial-defect verification of irradiated nuclear fuel assemblies using the DCVD
- 2014
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The Digital Cherenkov Viewing Device (DCVD) is a tool used by authority inspectors to verify irradiated nuclear fuel assemblies in wet storage by measuring the Cherenkov light emitted. The DCVD is approved by the IAEA for gross defect verification, and is one of the few inspection tools approved for partial defect verification.There is interest in adapting the DCVD to work in unattended mode, so that it can be used to verify large quantities of irradiated fuel assemblies prior to moving them to difficult-to-access storage locations. This work presents methods based on image analysis that can be used to reduce the effects of different types of distortions encountered when performing measurements with the DCVD. Implementing these methods will ensure that data of high quality is obtained. Verification prior to moving fuels to difficult-to-access storage may also require a dedicated measurement station to be built, and it is argued that by constructing these stations with the DCVD in mind, many distortions can be reduced or eliminated. Thus, by implementing safeguards-by-design, it is possible to ensure that the DCVD is used in near optimal conditions.
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| 8. |
- Fjalldal, S., et al.
(författare)
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Microstructural white matter alterations and hippocampal volumes are associated with cognitive deficits in craniopharyngioma
- 2018
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Ingår i: European Journal of Endocrinology. - : BIOSCIENTIFICA LTD. - 0804-4643 .- 1479-683X. ; 178:6, s. 577-587
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Tidskriftsartikel (refereegranskat)abstract
- Context: Patients with craniopharyngioma (CP) and hypothalamic lesions (HL) have cognitive deficits. Which neural pathways are affected is unknown. Objective: To determine whether there is a relationship between microstructural white matter (WM) alterations detected with diffusion tensor imaging (DTI) and cognition in adults with childhood-onset CP. Design: A cross-sectional study with a median follow-up time of 22 (6-49) years after operation. Setting: The South Medical Region of Sweden (2.5 million inhabitants). Participants: Included were 41 patients (24 women, amp;gt;= 17 years) surgically treated for childhood-onset CP between 1958-2010 and 32 controls with similar age and gender distributions. HI was found in 23 patients. Main outcome measures: Subjects performed cognitive tests and magnetic resonance imaging, and images were analyzed using DTI of uncinate fasciculus, fornix, cingulum, hippocampus and hypothalamus as well as hippocampal volumetry. Results: Right uncinate fasciculus was significantly altered (P amp;lt;= 0.01) Microstructural WM alterations in left ventral cingulum were significantly associated with worse performance in visual episodic memory, explaining approximately 50% of the variation. Alterations in dorsal cingulum were associated with worse performance in immediate, delayed recall and recognition, explaining 26-38% of the variation, and with visuospatial ability and executive function, explaining 19-29%. Patients who had smaller hippocampal volume had worse general knowledge (P = 0.028), and microstructural WM alterations in hippocampus were associated with a decline in general knowledge and episodic visual memory. Conclusions: A structure to function relationship is suggested between microstructural WM alterations in cingulum and in hippocampus with cognitive deficits in CP.
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