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| 2. |
- Dance, D, et al.
(författare)
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Breast dosimetry using high-resolution voxel phantoms
- 2005
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Ingår i: Radiation Protection Dosimetry. - : Oxford University Press (OUP). - 0144-8420 .- 1742-3406. ; 114:1-3, s. 359-363
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Tidskriftsartikel (refereegranskat)abstract
- A computer model of X-ray mammography has been developed, which uses quasi-realistic high-resolution voxel phantoms to simulate the breast. The phantoms have 400 μm voxels and simulate the three-dimensional distributions of adipose and fibroglandular tissues, Cooper's ligaments, ducts and skin and allow the estimation of dose to individual tissues. Calculations of the incident air kerma to mean glandular dose conversion factor, g, were made using a Mo/Mo spectrum at 28 kV for eight phantoms in the thickness range 40-80 mm and of varying glandularity. The values differed from standard tabulations used for breast dosimetry by up to 43%, because of the different spatial distribution of glandular tissue within the breast. To study this further, additional voxel phantoms were constructed, which gave variations of between 9 and 59% compared with standard values. For accurate breast dosimetry, it is therefore very important to take the distribution of glandular tissues into account. © The Author 2005. Published by Oxford University Press. All rights reserved.
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| 3. |
- Hammar, Petter, et al.
(författare)
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Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:4, s. 405-
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Tidskriftsartikel (refereegranskat)abstract
- Transcription factors mediate gene regulation by site-specific binding to chromosomal operators. It is commonly assumed that the level of repression is determined solely by the equilibrium binding of a repressor to its operator. However, this assumption has not been possible to test in living cells. Here we have developed a single-molecule chase assay to measure how long an individual transcription factor molecule remains bound at a specific chromosomal operator site. We find that the lac repressor dimer stays bound on average 5 min at the native lac operator in Escherichia coli and that a stronger operator results in a slower dissociation rate but a similar association rate. Our findings do not support the simple equilibrium model. The discrepancy with this model can, for example, be accounted for by considering that transcription initiation drives the system out of equilibrium. Such effects need to be considered when predicting gene activity from transcription factor binding strengths.
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| 4. |
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| 5. |
- Hunt, R, et al.
(författare)
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Calculation of the properties of digital mammograms using a computer simulation
- 2005
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Ingår i: Radiation Protection Dosimetry. - : Oxford University Press (OUP). - 0144-8420 .- 1742-3406. ; 114:1-3, s. 395-398
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Tidskriftsartikel (refereegranskat)abstract
- A Mote Carlo computer model of mammography has been developed to study and optimise the performance of digital mammographic systems. The program uses high-resolution voxel phantoms to model the breast, which simulate the adipose and fibroglandular tissues, Cooper's ligaments, ducts and skin in three dimensions. The model calculates the dose to each tissue, and also the quantities such as energy imparted to image pixels, noise per image pixel and scatter-to-primary (S/P) ratios. It allows studies of the dependence of image properties on breast structure and on position within the image. The program has been calibrated by calculating and measuring the pixel values and noise for a digital mammographic system. The thicknesses of two components of this system were unknown, and were adjusted to obtain a good agreement between measurement and calculation. The utility of the program is demonstrated with the calculations of the variation of the S/P ratio with and without a grid, and of the image contrast across the image of a 50-mm-thick breast phantom. © The Author 2005. Published by Oxford University Press. All rights reserved.
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| 6. |
- Hunt, R, et al.
(författare)
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Monte Carlo simulation of a mammographic test phantom
- 2005
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Ingår i: Radiation Protection Dosimetry. - : Oxford University Press (OUP). - 0144-8420 .- 1742-3406. ; 114:1-3, s. 432-435
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Tidskriftsartikel (refereegranskat)abstract
- A test phantom, including a wide range of mammographic tissue equivalent materials and test details, was imaged on a digital mammographic system. In order to quantify the effect of scatter on the contrast obtained for the test details, calculations of the scatter-to-primary ratio (S/P) have been made using a Monte Carlo simulation of the digital mammographic imaging chain, grid and test phantom. The results show that the S/P values corresponding to the imaging conditions used were in the range 0.084-0.126. Calculated and measured pixel values in different regions of the image were compared as a validation of the model and showed excellent agreement. The results indicate the potential of Monte Carlo methods in the image quality-patient dose process optimisation, especially in the assessment of imaging conditions not available on standard mammographic units. © The Author 2005. Published by Oxford University Press. All rights reserved.
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| 7. |
- Håkansson, Markus, et al.
(författare)
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Nodule detection in digital chest radiography: effect of nodule location.
- 2005
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Ingår i: Radiation protection dosimetry. - : Oxford University Press (OUP). - 0144-8420 .- 1742-3406. ; 114:1-3, s. 92-6
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Tidskriftsartikel (refereegranskat)abstract
- Most detection studies in chest radiography treat the entire chest image as a single background or divided into the two regions parenchyma and mediastinum. However, the different parts of the lung show great variations in attenuation and structure, leading to different amounts of quantum noise and scattered radiation as well as different complexity. Detailed data on the difference in detectability in the different regions are of importance. The purpose of this study was to quantify the difference in detectability between different regions of a chest image. The chest X ray was divided into six different regions, where each region was considered to be uniform in terms of detectability. Thirty clinical chest images were collected and divided into the different regions. Simulated designer nodules with a full-width-at-fifth-maximum of 10 mm but with varying contrast were added to the images. An equal number of images lacking pathology were included and a receiver operating characteristic (ROC) study was conducted with five observers. Results show that the image contrast needed to obtain a constant value of A(z) (area under an ROC curve) differs by more than a factor of four between different regions.
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| 8. |
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| 9. |
- Pavlov, Michael, et al.
(författare)
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Estimation of peptide elongation times from ribosome profiling spectra
- 2021
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Ingår i: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 49:9, s. 5124-5142
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Tidskriftsartikel (refereegranskat)abstract
- Ribosome profiling spectra bear rich information on translation control and dynamics. Yet, due to technical biases in library generation, extracting quantitative measures of discrete translation events has remained elusive. Using maximum likelihood statistics and data set from Escherichia coli we develop a robust method for neutralizing technical biases (e.g. base specific RNase preferences in ribosome-protected mRNA fragments (RPF) generation), which allows for correct estimation of translation times at single codon resolution. Furthermore, we validated the method with available datasets from E. coli treated with antibiotic to inhibit isoleucyl-tRNA synthetase, and two datasets from Saccharomyces cerevisiae treated with two RNases with distinct cleavage signatures. We demonstrate that our approach accounts for RNase cleavage preferences and provides bias-corrected translation times estimates. Our approach provides a solution to the long-standing problem of extracting reliable information about peptide elongation times from highly noisy and technically biased ribosome profiling spectra.
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| 10. |
- Sandborg, Michael, et al.
(författare)
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Comparison of clinical and physical measures of image quality in chest and pelvis computed radiography at different tube voltages
- 2006
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Ingår i: Medical Physics. - : Wiley. - 0094-2405. ; 33:11, s. 4169-4175
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this work was to study the dependence of image quality in digital chest and pelvis radiography on tube voltage, and to explore correlations between clinical and physical measures of image quality. The effect on image quality of tube voltage in these two examinations was assessed using two methods. The first method relies on radiologists' observations of images of an anthropomorphic phantom, and the second method was based on computer modeling of the imaging system using an anthropomorphic voxel phantom. The tube voltage was varied within a broad range (50-150 kV), including those values typically used with screen-film radiography. The tube charge was altered so that the same effective dose was achieved for each projection. Two x-ray units were employed using a computed radiography (CR) image detector with standard tube filtration and antiscatter device. Clinical image quality was assessed by a group of radiologists using a visual grading analysis (VGA) technique based on the revised CEC image criteria. Physical image quality was derived from a Monte Carlo computer model in terms of the signal-to-noise ratio, SNR, of anatomical structures corresponding to the image criteria. Both the VGAS (visual grading analysis score) and SNR decrease with increasing tube voltage in both chest PA and pelvis AP examinations, indicating superior performance if lower tube voltages are employed. Hence, a positive correlation between clinical and physical measures of image quality was found. The pros and cons of using lower tube voltages with CR digital radiography than typically used in analog screen-film radiography are discussed, as well as the relevance of using VGAS and quantum-noise SNR as measures of image quality in pelvis and chest radiography.
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