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Sökning: WFRF:(Jakobsson Mattias) > Lunds universitet

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1.
  • Säll, T., et al. (författare)
  • Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica
  • 2003
  • Ingår i: Journal of Evolutionary Biology. - : John Wiley & Sons Inc.. - 1010-061X .- 1420-9101. ; 16:5, s. 1019-1029
  • Tidskriftsartikel (refereegranskat)abstract
    • DNA sequencing was performed on up to 12 chloroplast DNA regions [giving a total of 4288 base pairs (bp) in length] from the allopolyploid Arabidopsis suecica (48 accessions) and its two parental species, A. thaliana (25 accessions) and A. arenosa (seven accessions). Arabidopsis suecica was identical to A. thaliana at all 93 sites where A. thaliana and A. arenosa differed, thus showing that A. thaliana is the maternal parent of A. suecica. Under the assumption that A. thaliana and A. arenosa separated 5 million years ago, we estimated a substitution rate of 2.9 x 10(-9) per site per year in noncoding single copy sequence. Within A. thaliana we found 12 substitution (single bp) and eight insertion/deletion (indel) polymorphisms, separating the 25 accessions into 15 haplotypes. Eight of the A. thaliana accessions from central Sweden formed one cluster, which was separated from a cluster consisting of central European and extreme southern Swedish accessions. This latter cluster also included the A. suecica accessions, which were all identical except for one 5 bp indel. We interpret this low level of variation as a strong indication that A. suecica effectively has a single origin, which we dated at 20 000 years ago or more.
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2.
  • Gutte, Henrik, et al. (författare)
  • Automated interpretation of PET/CT images in patients with lung cancer.
  • 2007
  • Ingår i: Nuclear Medicine Communications. - 1473-5628. ; 28:2, s. 79-84
  • Tidskriftsartikel (refereegranskat)abstract
    • Purpose: To develop a completely automated method based on image processing techniques and artificial neural networks for the interpretation of combined [18F]fluorodeoxyglucose (FDG) positron emission tomography (PET) and computed tomography (CT) images for the diagnosis and staging of lung cancer. Methods: A total of 87 patients who underwent PET/CT examinations due to suspected lung cancer comprised the training group. The test group consisted of PET/CT images from 49 patients suspected with lung cancer. The consensus interpretations by two experienced physicians were used as the 'gold standard' image interpretation. The training group was used in the development of the automated method. The image processing techniques included algorithms for segmentation of the lungs based on the CT images and detection of lesions in the PET images. Lung boundaries from the CT images were used for localization of lesions in the PET images in the feature extraction process. Eight features from each examination were used as inputs to artificial neural networks trained to classify the images. Thereafter, the performance of the network was evaluated in the test set. Results: The performance of the automated method measured as the area under the receiver operating characteristic curve, was 0.97 in the test group, with an accuracy of 92%. The sensitivity was 86% at a specificity of 100%. Conclusions: A completely automated method using artificial neural networks can be used to detect lung cancer with such a high accuracy that the application as a clinical decision support tool appears to have significant potential.
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3.
  • Holm, Alexander, et al. (författare)
  • Patients' perspective on prostatic artery embolization : A qualitative study
  • 2021
  • Ingår i: SAGE Open Medicine. - : SAGE Open. - 2050-3121. ; 9, s. 1-6
  • Tidskriftsartikel (refereegranskat)abstract
    • Objectives: The aim was to describe the patients' experience of undergoing prostatic artery embolization.Methods: A retrospective qualitative interview study was undertaken with 15 patients of mean age 73 years who had undergone prostatic artery embolization with a median duration of 210 min at two medium sized hospitals in Sweden. The reasons for conducting prostatic artery embolization were clean intermittent catheterization (n = 4), lower urinary tract symptoms (n = 10) or haematuria (n = 1). Data were collected through individual, semi-structured telephone interviews 1-12 months after treatment and analysed using qualitative content analysis.Results: Four categories with sub-categories were formulated to describe the results: a diverse experience; ability to control the situation; resumption of everyday activities and range of opinions regarding efficacy of outcomes. Overall, the patients described the procedure as painless, easy and interesting and reported that while the procedure can be stressful, a calm atmosphere contributed to achieving a good experience. Limitations on access to reliable information before, during and after the procedure were highlighted as a major issue. Practical ideas for improving patient comfort during the procedure were suggested. Improved communications between treatment staff and patients were also highlighted. Most patients could resume everyday activities, some felt tired and bruising caused unnecessary worry for a few. Regarding functional outcome, some patients described substantial improvement in urine flow while others were satisfied with regaining undisturbed night sleep. Those with less effect were considering transurethral resection of the prostate as a future option. Self-enrolment to the treatment and long median operation time may have influenced the results.Conclusions: From the patients' perspective, prostatic artery embolization is a well-tolerated method for treating benign prostate hyperplacia.
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4.
  • Jakobsson, Mattias, et al. (författare)
  • A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers
  • 2006
  • Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 23:6, s. 1217-1231
  • Tidskriftsartikel (refereegranskat)abstract
    • A coalescent-based method was used to investigate the origins of the allotetraploid Arabidopsis suecica, using 52 nuclear microsatellite loci typed in eight individuals of A. suecica and 14 individuals of its maternal parent Arabidopsis thaliana, and four short fragments of genomic DNA sequenced in a sample of four individuals of A. suecica and in both its parental species A. thaliana and Arabidopsis arenosa. All loci were variable in A. thaliana but only 24 of the 52 microsatellite loci and none of the four sequence fragments were variable in A. suecica. We explore a number of possible evolutionary scenarios for A. suecica and conclude that it is likely that A. suecica has a recent, unique origin between 12,000 and 300,000 years ago. The time estimates depend strongly on what is assumed about population growth and rates of mutation. When combined with what is known about the history of glaciations, our results suggest that A. suecica originated south of its present distribution in Sweden and Finland and then migrated north, perhaps in the wake of the retreating ice.
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5.
  • Jakobsson, Mattias, et al. (författare)
  • Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana
  • 2007
  • Ingår i: Theoretical and Applied Genetics. - : Springer. - 0040-5752 .- 1432-2242. - 0040-5752 ; 114:2, s. 223-235
  • Tidskriftsartikel (refereegranskat)abstract
    • The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated-such as the position of a locus within the chromosome, or imperfect repeats-appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate.
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6.
  • Jakobsson, Mattias, et al. (författare)
  • Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana
  • 2007
  • Ingår i: Theoretical And Applied Genetics. - : Springer Science and Business Media LLC. - 0040-5752 .- 1432-2242. ; 114:2, s. 223-235
  • Tidskriftsartikel (refereegranskat)abstract
    • The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated-such as the position of a locus within the chromosome, or imperfect repeats-appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate.
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7.
  • Jakobsson, Mattias (författare)
  • Genome Divergence in Progress - a population genetic analysis of the allopolyploid Arabidopsis suecica and its maternal parent A. thaliana
  • 2005
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The evolutionary history of the allotetraploid Arabidopsis suecica and its maternal parent Arabidopsis thaliana is analyzed in the thesis in terms of genetic variation in the natural populations of the two species. The earliest phase of the speciation event in which the genomes of A. thaliana and A. suecica are in the process of diverging was investigated using population genetic methods. Evolutionary and demographic hypotheses were tested on the basis of sequence and microsatellite variation in the nuclear and chloroplast genomes. It was shown that the maternally inherited chloroplast originated in all investigated A. suecica individuals from A. thaliana, identifying A. thaliana as A. suecica's maternal parent. A Bayesian multi-locus method based on coalescent theory was developed to infer the evolutionary history of polyploids in general and specifically of A. suecica. It provides a rigorous statistical framework allowing the confidence in one's conclusions to be quantified. The origins of allopolyploid species, in contrast to those of most species, can be considered to be well defined discrete events. Both the nuclear and the chloroplast genome of A. suecica were shown to have a single origin, implying there to be a single origin for the entire species. Its origin was estimated to have been 10 thousand to 65 thousand years ago. The A. thaliana and the A. suecica populations were shown to both be genetically structured, although the A. thaliana population, unlike the A. suecica population, clearly was geographically structured too. A. suecica and A. thaliana were also found to differ in terms of Linkage Disequilibrium, it extends further and the levels are higher in A. suecica than in A. thaliana. These findings showed that a species of recent, single origin has quite different patterns of genetic variation than of more distant origin. In the first genome-wide study ever of sequence polymorphisms in a eukaryote organism, here A. thaliana, it was found that the data failed to fit standard neutral models. This means that attempts to infer natural selection on the basis of polymorphism data will require genome-wide surveys of polymorphism in order to identify regions that are anomalous. Certain theoretical models of microsatellite evolution were shown to fit the distribution of mononucleotide microsatellites in the A. thaliana genome. These models were also able to predicted empirical levels of microsatellite variation in the A. thaliana chloroplast genome. This thesis is based on the following papers: I. Säll, T., Jakobsson, M., Lind-Halldén, C. & Halldén, C. (2003) Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica. J. Evol. Biol. 16: 1019 1029. II. Jakobsson, M., Säll, T., Lind-Halldén, C. & Halldén, C. The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica. (Submitted). III. Jakobsson, M., Hagenblad, J., Tavaré, S., Nordborg, M., Halldén, C., Säll, T. & Lind-Halldén, C. A recent unique origin of the allotetraploid species Arabidopsis suecica evidence from nuclear DNA markers. (Manuscript). IV. Jakobsson, M., Säll, T., Halldén, C. & Lind-Halldén, C. Genome evolution in progress: Linkage disequilibrium and population structure in Arabidopsis suecica and A. thaliana. (Manuscript). V. Nordborg, M., Hu, T., Ishino, Y., Jhaveri, J., Toomajian, C., Zheng, H., Tomer, E., Calabrese, P., Gladstone, J., Goyal, R., Jakobsson, M., Kim, S., Morozov, Y., Padhukasahasram, B., Plagnol, V., Rosenberg, N., A., Shah, C., Wall, J., Zhao, K., Kalbfleisch, T., Schultz, V., Kreitman, M. & Bergelson, J. (2005) The Pattern of Polymorphism in Arabidopsis thaliana. PLoS Biology (in Press). VI. Jakobsson, M., Säll, T., Lind-Halldén, C. & Halldén, C. Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana. (Submitted).
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8.
  • Jakobsson, Mattias, et al. (författare)
  • The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica.
  • 2007
  • Ingår i: Journal of evolutionary biology. - : Wiley. - 1420-9101 .- 1010-061X. ; 20:1, s. 104-121
  • Tidskriftsartikel (refereegranskat)abstract
    • The evolutionary history of the common chloroplast (cp) genome of the allotetraploid Arabidopsis suecica and its maternal parent A. thaliana was investigated by sequencing 50 fragments of cpDNA, resulting in 98 polymorphic sites. The variation in the A. suecica sample was small, in contrast to that of the A. thaliana sample. The time to the most recent common ancestor (T-MRCA) of the A. suecica cp genome alone was estimated to be about one 37th of the T-MRCA of both the A. thaliana and A. suecica cp genomes. This corresponds to A. suecica having a MRCA between 10 000 and 50 000 years ago, suggesting that the entire species originated during, or before, this period of time, although the estimates are sensitive to assumptions made about population size and mutation rate. The data was also consistent with the hypothesis of A. suecica being of single origin. Isolation-by-distance and population structure in A. thaliana depended upon the geographical scale analysed; isolation-by-distance was found to be weak on the global scale but locally pronounced. Within the genealogical cp tree of A. thaliana, there were indications that the root of the A. suecica species is located among accessions of A. thaliana that come primarily from central Europe. Selective neutrality of the cp genome could not be rejected, despite the fact that it contains several completely linked protein-coding genes.
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9.
  • Nordborg, M, et al. (författare)
  • The pattern of polymorphism in Arabidopsis thaliana
  • 2005
  • Ingår i: PLoS Biology. - : Public Library of Science (PLoS). - 1545-7885. ; 3:7, s. 1289-1299
  • Tidskriftsartikel (refereegranskat)abstract
    • We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.
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10.
  • Sadik, May, 1970, et al. (författare)
  • A new computer-based decision-support system for the interpretation of bone scans
  • 2006
  • Ingår i: Nucl Med Commun. - 0143-3636. ; 27:5, s. 417-423
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE: To develop a completely automated method, based on image processing techniques and artificial neural networks, for the interpretation of bone scans regarding the presence or absence of metastases. METHODS: A total of 200 patients, all of whom had the diagnosis of breast or prostate cancer and had undergone bone scintigraphy, were studied retrospectively. Whole-body images, anterior and posterior, were obtained after injection of 99mTc-methylene diphosphonate. The study material was randomly divided into a training group and a test group, with 100 patients in each group. The training group was used in the process of developing the image analysis techniques and to train the artificial neural networks. The test group was used to evaluate the automated method. The image processing techniques included algorithms for segmentation of the head, chest, spine, pelvis and bladder, automatic thresholding and detection of hot spots. Fourteen features from each examination were used as input to artificial neural networks trained to classify the images. The interpretations by an experienced physician were used as the 'gold standard'. RESULTS: The automated method correctly identified 28 of the 31 patients with metastases in the test group, i.e., a sensitivity of 90%. A false positive classification of metastases was made in 18 of the 69 patients not classified as having metastases by the experienced physician, resulting in a specificity of 74%. CONCLUSION: A completely automated method can be used to detect metastases in bone scans. Future developments in this field may lead to clinically valuable decision-support tools.
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