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- Agirre, Jon, et al.
(författare)
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The CCP4 suite: integrative software for macromolecular crystallography
- 2023
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Ingår i: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 79, s. 449-461
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Tidskriftsartikel (refereegranskat)abstract
- The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
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- Brynolfsson, Patrik, et al.
(författare)
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Tensor-valued diffusion magnetic resonance imaging in a radiotherapy setting
- 2022
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Ingår i: Physics and imaging in radiation oncology. - : Elsevier BV. - 2405-6316. ; 24, s. 144-151
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Tidskriftsartikel (refereegranskat)abstract
- Background and purposeDiagnostic information about cell density variations and microscopic tissue anisotropy can be gained from tensor-valued diffusion magnetic resonance imaging (MRI). These properties of tissue microstructure have the potential to become novel imaging biomarkers for radiotherapy response. However, tensor-valued diffusion encoding is more demanding than conventional encoding, and its compatibility with MR scanners that are dedicated to radiotherapy has not been established. Thus, our aim was to investigate the feasibility of tensor-valued diffusion MRI with radiotherapy dedicated MR equipment.Material and methodsA tensor-valued diffusion protocol was implemented, and five healthy volunteers were scanned with different resolutions using conventional head coil and radiotherapy coil setup with fixation masks. Signal-to-noise-ratio (SNR) was evaluated to assess the risk of signal bias due to rectified noise floor. We also evaluated the repeatability and reproducibility of the microstructure parameters. One patient with brain metastasis was scanned to investigate the image quality and the transferability of the setup to diseased tissue.ResultsA resolution of 3×3×3 mm3 provided images with SNR>3 for 93% of the voxels using radiotherapy coil setup. The parameter maps and repeatability characteristics were comparable to those observed with a conventional head coil. The patient evaluation demonstrated successful parameter analysis also in tumor tissue, with SNR>3 for 93% of the voxels.ConclusionWe demonstrate that tensor-valued diffusion MRI is compatible with radiotherapy fixation masks and coil setup for investigations of microstructure parameters. The reported reproducibility may be used to plan future investigations of imaging biomarkers in brain cancer radiotherapy.
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- Elias, Augusto E., et al.
(författare)
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MR Spectroscopy Using Normalized and Non-normalized Metabolite Ratios for Differentiating Recurrent Brain Tumor from Radiation Injury
- 2011
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Ingår i: Academic Radiology. - : Elsevier BV. - 1878-4046 .- 1076-6332. ; 18:9, s. 1101-1108
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Tidskriftsartikel (refereegranskat)abstract
- Rationale and Objectives: To compare the ability of normalized versus non-normalized metabolite ratios to differentiate recurrent brain tumor from radiation injury using magnetic resonance spectroscopy (MRS) in previously treated patients. Materials and Methods: Twenty-five patients with previous diagnosis of primary intracranial neoplasm confirmed with biopsy/resection, previously treated with radiation therapy (range, 54-70 Gy) with or without chemotherapy and new contrast enhancing lesion on a 1.5 T magnetic resonance imaging at the site of the primary neoplasm participated in this retrospective study. After MRS, clinical, radiological, and histopathology data were used to classify new contrast-enhancing lesions as either recurrent neoplasm or radiation injury. Volume of interest included both the lesion and normal-appearing brain on the contralateral side. Non-normalized metabolic ratios were calculated from choline (Cho), creatine (Cr), and N-acetylaspartate (NAA) spectroscopic values obtained within the contrast-enhancing lesion: Cho/Cr, NAA/Cr, and Cho/NAA. Normalized ratios were calculated using the metabolic values from the contralateral normal side: Cho/normal creatinine (nCr), Cho/normal N-acetylaspartate (nNAA), Cho/normal choline, NAA/nNAA, NAA/nCr, and Cr/nCr. Results were correlated with the final diagnosis by Wilcoxon rank-sum analysis. Results: Two of three non-normalized ratios, Cho/NAA (sensitivity 86%, specificity 90%) and NAA/Cr (sensitivity 93%, specificity 70%) significantly associated with tumor recurrence even after correcting for multiple comparisons. Of the six normalized ratios, only Cho/nNAA significantly correlated with tumor recurrence (sensitivity 73%, specificity 40%), but did not remain significant after correcting for multiple comparisons. Conclusion: Cho/NAA and NAA/Cr were the two ratios with the best discriminating ability and both had better discriminating ability than their corresponding normalized ratios (Area under the curve = 0.92 versus 0.77, AUC= 0.85 vs. 0.66), respectively.
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