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1.
  • Ericsson, Olle, et al. (författare)
  • Clinical validation of a novel automated cell-free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma.
  • 2019
  • Ingår i: Prenatal diagnosis. - 1097-0223. ; 39:11, s. 1011-1015
  • Tidskriftsartikel (refereegranskat)abstract
    • To evaluate clinical performance of a new automated cell-free (cf)DNA assay in maternal plasma screening for trisomies 21, 18, and 13, and to determine fetal sex.Maternal plasma samples from 1200 singleton pregnancies were analyzed with a new non-sequencing cfDNA method, which is based on imaging and counting specific chromosome targets. Reference outcomes were determined by either cytogenetic testing, of amniotic fluid or chorionic villi, or clinical examination of neonates.The samples examined included 158 fetal aneuploidies. Sensitivity was 100% (112/112) for trisomy 21, 89% (32/36) for trisomy 18, and 100% (10/10) for trisomy 13. The respective specificities were 100%, 99.5%, and 99.9%. There were five first pass failures (0.4%), all in unaffected pregnancies. Sex classification was performed on 979 of the samples and 99.6% (975/979) provided a concordant result.The new automated cfDNA assay has high sensitivity and specificity for trisomies 21, 18, and 13 and accurate classification of fetal sex, while maintaining a low failure rate. The study demonstrated that cfDNA testing can be simplified and automated to reduce cost and thereby enabling wider population-based screening.
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2.
  • Gustafsson, Harald, et al. (författare)
  • Den dubbla blicken. En inledning
  • 2007
  • Ingår i: Den dubbla blicken. Historia i de nordiska samhällena. - Sekel Bokförlag. - 978-91-85767-00-7 ; s. 7-26
  • Bokkapitel (övrigt vetenskapligt)
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3.
4.
  • Johansson, Karl-Axel, et al. (författare)
  • The quality assurance process for the ARTSCAN head and neck study - a practical interactive approach for QA in 3DCRT and IMRT.
  • 2008
  • Ingår i: Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology. - 0167-8140. ; 87:2, s. 290-9
  • Tidskriftsartikel (refereegranskat)abstract
    • Aim: This paper describes the quality assurance (QA) work performed in the Swedish multicenter ARTSCAN (Accelerated RadioTherapy of Squamous cell CArcinomas in the head and Neck) trial to guarantee high quality in a multicenter study which involved modern radiotherapy such as 3DCRT or IMRT. Materials and methods: The study was closed in June 2006 with 750 randomised patients. Radiation therapy-related data for every patient were sent by each participating centre to the QA office where all trial data were reviewed, analysed and stored. In case of any deviation from the protocol, an interactive process was started between the QA office and the local responsible clinician and/or physicist to increase the compliance to the protocol for future randomised patients. Meetings and workshops were held on a regular basis for discussions on various trial-related issues and for the QA office to report on updated results. Results and discussion: This review covers the 734 patients out of a total of 750 who had entered the study. Deviations early in the study were corrected so that the overall compliance to the protocol was very high. There were only negligible variations in doses and dose distributions to target volumes for each specific site and stage. The quality of the treatments was high. Furthermore, an extensive database of treatment parameters was accumulated for future dose-volume vs. endpoint evaluations. Conclusions: This comprehensive QA programme increased the probability to draw firm conclusions from our study and may serve as a concept for QA work in future radiotherapy trials where comparatively small effects are searched for in a heterogeneous tumour population.
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5.
  • Nyberg, Lena K., et al. (författare)
  • A single-step competitive binding assay for mapping of single DNA molecules
  • 2012
  • Ingår i: Biochemical and Biophysical Research Communications. - 1090-2104 .- 0006-291X. ; 417:1, s. 404-408
  • Tidskriftsartikel (refereegranskat)abstract
    • Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
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6.
  • Nyberg, Lena K., et al. (författare)
  • A single-step competitive binding assay for mapping of single DNA molecules
  • 2012
  • Ingår i: Biochemical and Biophysical Research Communications - BBRC. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.</p>
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7.
  • Persson, Fredrik, et al. (författare)
  • USING SIMULATION TO DETERMINE THE SAFETY STOCK LEVEL FOR INTERMITTENT DEMAND
  • 2017
  • Ingår i: 2017 WINTER SIMULATION CONFERENCE (WSC). - IEEE. - 978-1-5386-3428-8 ; s. 3768-3779
  • Konferensbidrag (refereegranskat)abstract
    • <p>Safety stock calculations are difficult for products with intermittent demand, long production lead times, and high monetary values. Theoretically, forecasts can be used to reduce the need for safety stocks. A high precision forecast minimizes the need for safety stock and forecast evaluation measurements can be used to calculate the safety stock level. However, a more realistic determination of safety stock levels can he obtained by simulation. In this paper, simulation is used to model and experiment on a case with three end products in order to determine the relationship between safety stock levels and service levels. Also, a comparison is made with theoretically calculated safety stocks to see how well basic theoretical models for safety stock calculations fulfill the requirements of service level. The result is that simulation can provide a much more accurate determination of safety stock levels for intermittent demands than theoretical calculations.</p>
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8.
  • Alizadehheidari, Mohammadreza, et al. (författare)
  • Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
  • 2015
  • Ingår i: Macromolecules. - The American Chemical Society (ACS). - 0024-9297. ; 48:3, s. 871-878
  • Tidskriftsartikel (refereegranskat)abstract
    • Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
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9.
  • Alizadehheidari, Mohammadreza, et al. (författare)
  • Nanoconfined Circular and Linear DNA : Equilibrium Conformations and Unfolding Kinetics
  • 2015
  • Ingår i: Macromolecules. - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878
  • Tidskriftsartikel (refereegranskat)abstract
    • <p>Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.</p>
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10.
  • Alizadehheidari, Mohammadreza, et al. (författare)
  • Nanoconfined Circular DNA
  • 2014
  • Ingår i: Biophysical Journal. - 0006-3495 .- 1542-0086. ; 106:2, s. 274A-274A
  • Tidskriftsartikel (övrigt vetenskapligt)abstract
    • <p>Nanofluidic channels have become a versatile tool to manipulate single DNA molecules. They allow investigation of confined single DNA molecules from a fundamental polymer physics perspective as well as for example in DNA barcoding techniques.</p>
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