| 1. |
- Dahlberg, Johan, et al.
(författare)
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Arteria : An automation system for a sequencing core facility
- 2019
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Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 8:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an automation system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities.Findings: Arteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/.Conclusions: We describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.
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| 2. |
- La Fleur, Linnea, et al.
(författare)
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Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11
- 2019
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Ingår i: Lung Cancer. - : Elsevier BV. - 0169-5002 .- 1872-8332. ; 130, s. 50-58
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Non-small cell lung cancer (NSCLC) is a heterogeneous disease with unique combinations of somatic molecular alterations in individual patients, as well as significant differences in populations across the world with regard to mutation spectra and mutation frequencies. Here we aim to describe mutational patterns and linked clinical parameters in a population-based NSCLC cohort.MATERIALS AND METHODS: Using targeted resequencing the mutational status of 82 genes was evaluated in a consecutive Swedish surgical NSCLC cohort, consisting of 352 patient samples from either fresh frozen or formalin fixed paraffin embedded (FFPE) tissues. The panel covers all exons of the 82 genes and utilizes reduced target fragment length and two-strand capture making it compatible with degraded FFPE samples.RESULTS: We obtained a uniform sequencing coverage and mutation load across the fresh frozen and FFPE samples by adaption of sequencing depth and bioinformatic pipeline, thereby avoiding a technical bias between these two sample types. At large, the mutation frequencies resembled the frequencies seen in other western populations, except for a high frequency of KRAS hotspot mutations (43%) in adenocarcinoma patients. Worse overall survival was observed for adenocarcinoma patients with a mutation in either TP53, STK11 or SMARCA4. In the adenocarcinoma KRAS-mutated group poor survival appeared to be linked to concomitant TP53 or STK11 mutations, and not to KRAS mutation as a single aberration. Similar results were seen in the analysis of publicly available data from the cBioPortal. In squamous cell carcinoma a worse prognosis could be observed for patients with MLL2 mutations, while CSMD3 mutations were linked to a better prognosis.CONCLUSION: Here we have evaluated the mutational status of a NSCLC cohort. We could not confirm any survival impact of isolated driver mutations. Instead, concurrent mutations in TP53 and STK11 were shown to confer poor survival in the KRAS-positive adenocarcinoma subgroup.
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| 3. |
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| 4. |
- Ander, S J, et al.
(författare)
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Growth and function of human parathyroid tissue transplanted to athymic mice.
- 1997
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Ingår i: Journal of endocrinological investigation. - 0391-4097. ; 20:11, s. 640-7
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Tidskriftsartikel (refereegranskat)abstract
- The morphology, cell proliferation and function of transplanted normal, hyperplastic and adenomatous human parathyroid tissue was studied after transplantation to athymic mice. The iPTH was evaluated in relation to morphology. Human parathyroid tissue collected during surgery for hyperparathyroidism was implanted subcutaneously into athymic mice (nu/nu-BALB/cA) and was analysed 1, 4, 7 and 12 weeks after transplantation. The transplants were examined by light and electron microscopy and by autoradiography after continuous infusion of 3H-thymidine. The relative amount of viable tissue was evaluated using a computer image analysing programme. Graft function was evaluated by measuring human iPTH in mouse serum. A transplant take ratio of 93% was observed. The proliferation rate in adenoma grafts at 12 weeks after transplantation was five and fifteen times that observed in normal and hyperplastic transplants, respectively. In normal and adenoma groups, a continuous increase in iPTH concentrations was observed, but in the hyperplastic group the iPTH remained on the same level. The secretion of iPTH in relation to the amount of transplanted tissue and the fraction of viable tissue was at the same level at 12 weeks in normal and adenomatous grafted animals. In conclusion, human parathyroid tissue was successfully transplanted and maintained its original structure. The growth potential, but not the iPTH secretion, was significantly higher in adenoma grafts compared to grafts from hyperplastic and normal glands.
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| 5. |
- Ander, S J, et al.
(författare)
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Revascularisation of human parathyroid tissue transplanted to athymic mice.
- 1997
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Ingår i: APMIS : acta pathologica, microbiologica, et immunologica Scandinavica. - 0903-4641. ; 105:12, s. 931-40
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Tidskriftsartikel (refereegranskat)abstract
- The revascularisation process of transplanted human normal, hyperplastic and adenomatous parathyroid tissue was analysed at 2 and 4 days and 1, 2, 4, 7 and 12 weeks after transplantation to athymic mice. The transplants were examined by light and electron microscopy, immunohistochemistry and autoradiography. Vessels were detected by monoclonal antibodies specific for mouse and human endothelial cells. Immunohistochemistry demonstrated ingrowth of vessels from the host into the transplant and at one week numerous capillary sprouts were observed in the peripheral parts of the transplants. During the first week, peak levels of proliferation (labelling index) were observed in endothelial cells and capsular fibroblasts, and the proliferative capacity of endothelial cells was most pronounced in adenoma transplants. Fenestrated capillaries were observed in hyperplastic and adenomatous transplants, but not in transplants of normal tissue. In conclusion, revascularisation of transplanted human parathyroid tissue is enabled by ingrowth of vessels from the host into the transplant. The proliferative capacity of endothelial cells is higher and the process of maturation is faster in hyperplastic and adenomatous tissue compared to normal tissue.
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| 6. |
- Forsblad-D’Elia, Helena, et al.
(författare)
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Biomechanical properties of common carotid arteries assessed by circumferential 2D strain and β stiffness index in patients with ankylosing spondylitis
- 2021
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Ingår i: Journal of Rheumatology. - 0315-162X. ; 48:3, s. 352-360
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Tidskriftsartikel (refereegranskat)abstract
- Objective. Ankylosing spondylitis (AS) is associated with an elevated risk of cardiovascular disease (CVD) related to atherosclerosis, preceded by arterial stiffness. We aimed to examine common carotid artery (CCA) biomechanical properties using ultrasound to calculate β stiffness index (indicating arterial stiffness) and, a more recently developed technique, 2-dimensional (2D) speckle tracking strain (indicating arterial motion and deformation, strain) to (1) compare with age- and sex-matched controls, and (2) analyze relationships between strain and stiffness with disease characteristics and traditional risk factors for CVD in patients with AS. Methods. In this cross-sectional study, a cohort of 149 patients with AS, mean age 55.3 ± 11.2 years, 102 (68.5%) men, and 146 (98%) HLA-B27–positive, were examined. Bilateral CCA were examined for circumferential 2D strain and β stiffness index. A subgroup of 46 patients was compared with 46 age- and sex-matched controls, both groups without hypertensive disease, diabetes, myocardial infarction, or stroke. Results. Mean bilateral circumferential 2D strain was lower in AS patients compared with controls (7.9 ± 2.6% vs 10.3 ± 1.9%, P < 0.001), whereas mean bilateral β stiffness index was higher (13.1 ± 1.7 mmHg/mm vs 12.3 ± 1.3 mmHg/mm, P = 0.02). In multivariable linear regression analyses, strain was associated with age, erythrocyte sedimentation rate, history of anterior uveitis, and treatment with conventional synthetic disease-modifying antirheumatic drugs (DMARD) and/or biological DMARD (R2 0.33), while stiffness was associated with age (R2 0.19). Conclusion. Both CCA circumferential 2D strain and β stiffness index differed between patients with AS and controls. Strain was associated with AS-related factors and age, whereas only age was associated with stiffness, suggesting that the obtained results reflect different pathogenic vascular processes.
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| 7. |
- Forsblad-d'Elia, Helena, et al.
(författare)
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Biomechanical properties of common carotid arteries assessed by circumferential two-dimensional strain and β stiffness index in patients with ankylosing spondylitis
- 2021
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Ingår i: Journal of Rheumatology. - : The Journal of Rheumatology. - 0315-162X .- 1499-2752. ; 48:3, s. 352-360
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: Ankylosing spondylitis (AS) is associated with an elevated risk of cardiovascular disease (CVD) related to atherosclerosis, preceded by arterial stiffness. We aimed to examine common carotid artery (CCA) biomechanical properties using ultrasound to calculate β stiffness index (indicating arterial stiffness) and, a more recently developed technique, two-dimensional (2D) speckle tracking strain (indicating arterial motion and deformation, strain) to 1) compare with age- and sex-matched controls and to 2) analyze relationships between strain and stiffness with disease characteristics and traditional risk factors for CVD in AS patients.METHODS: In this cross-sectional study, a cohort of 149 patients with AS, mean age 55.3±11.2 years, 102(68.5%) men, 146 (98%) HLA-B27 positive, were examined. Bilateral CCAs were examined for circumferential 2D strain and β stiffness index. A subgroup of 46 patients were compared with 46 age- and sex-matched controls, both groups without hypertensive disease, diabetes, myocardial infarction or stroke.RESULTS: Mean bilateral circumferential 2D strain was lower in AS patients compared with controls, 7.9±2.6% vs 10.3±1.9%, p<0.001 whereas mean bilateral β stiffness index was higher, 13.1±1.6mmHg/mm vs 12.3±1.3mmHg/mm, p=0.018. In multivariable linear regression analyses strain was associated with age, erythrocyte sedimentation rate, history of anterior uveitis and treatment with csDMARD and/or bDMARD (R2 0.33), while stiffness was associated with age (R2 0.19).CONCLUSION: Both CCA circumferential 2D strain and β stiffness index differed between AS patients and controls. Strain was associated with AS-related factors and age while stiffness with age, suggesting that the obtained results reflect different pathogenic vascular processes.
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| 8. |
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| 9. |
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| 10. |
- Ljung, Lotta, et al.
(författare)
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Patterns of comorbidity and disease characteristics among patients with ankylosing spondylitis : a cross-sectional study
- 2018
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Ingår i: Clinical Rheumatology. - : Springer London. - 0770-3198 .- 1434-9949. ; 37:3, s. 647-653
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Tidskriftsartikel (refereegranskat)abstract
- The knowledge of the development of comorbidities in patients with ankylosing spondylitis (AS) is limited. The aim of this study was to analyse associations between AS disease characteristics and comorbidity and to evaluate patterns of comorbidities in patients with AS. Patients with AS, fulfilling the modified New York Criteria, were identified (n =3D 346, mean age 56 +/- 15 years, 75% men, 99% HLA B27 positive). Through a review of the patient records, data on disease activity parameters, laboratory results, disease manifestations, and diagnoses of any clinically significant comorbidity was obtained. Four categories of comorbidities of interest were identified: A. arrhythmias, conduction disorders, and valvular heart disease; B. atherosclerosis and atherosclerotic CVD; C. spinal and non-spinal fractures; and D. obstructive sleep apnoea syndrome. Associations between AS disease characteristics and comorbidities in categories were assessed in logistic regression models. Differences in proportions of comorbidities was analysed using two-sided chi-square. Age was associated with all four categories of comorbidities, and male sex with arrhythmias, conduction disorders, valvular heart disease, and obstructive sleep apnoea syndrome. Early disease onset and long disease duration, respectively, were associated with arrhythmias, conduction disorders, and valvular heart disease. Obstructive sleep apnoea syndrome was associated with features of the metabolic syndrome. Patients with atherosclerotic cardiovascular disease had an increased risk of most other comorbidities, similar to, but more pronounced than patients with arrhythmias, conduction disorders and valvular heart disease. Comorbid conditions motivate clinical awareness among patients with AS. Longitudinal studies are needed to establish preventive measures.
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