| 1. |
- Li, Haoyuan, et al.
(författare)
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Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source
- 2020
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Ingår i: Scientific Data. - : NATURE RESEARCH. - 2052-4463. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 mu m x 1.7 mu m full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.
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| 2. |
- Alvfeldt, G, et al.
(författare)
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Radiology reporting in rectal cancer using MRI: adherence to national template for structured reporting
- 2022
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Ingår i: Acta radiologica (Stockholm, Sweden : 1987). - : SAGE Publications. - 1600-0455 .- 0284-1851. ; 63:12, s. 1603-1612
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Tidskriftsartikel (refereegranskat)abstract
- In 2014, a national workshop program was initiated and a reporting template and manual for rectal cancer primary staging using magnetic resonance imaging (MRI) was introduced and made available by the national Swedish Colorectal Cancer Registry. Purpose To evaluate the effect of the national template program by identify if there was a gap between the content in Swedish MRI reports from 2016 and the national reporting template from 2014. The aim was to explore and compare differences in content in reporting practice in different hospitals in relation to the national reporting template, with focus on: (i) identifying any implementational differences in reporting styles; and (ii) evaluating if reporting completeness vary based on such implementational differences. Material and Methods A total of 250 MRI reports from 10 hospitals in four healthcare regions in Sweden were collected. Reports were analyzed using qualitative content analysis with a deductive thematic coding scheme based on the national reporting template. Results Three different implemented reporting styles were identified with variations of content coverage in relation to the template: (i) standardized and structured protocol (reporting style A); (ii) standardized semi-structured free-text (reporting style B); and (iii) regular free-text (reporting style C). The relative completeness of reporting practice of rectal cancer staging in relation to the national reporting template were 92.9% for reporting style A, 77.5% for reporting style B, and 63.9% for reporting style C. Conclusion The implementation of template-based reporting according to reporting style A is a key factor to conform to evidence-based practice for rectal cancer reporting using MRI.
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| 3. |
- Alvfeldt, G, et al.
(författare)
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Rectal cancer staging using MRI: adherence in reporting to evidence-based practice
- 2020
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Ingår i: Acta radiologica (Stockholm, Sweden : 1987). - : SAGE Publications. - 1600-0455 .- 0284-1851. ; 61:11, s. 1463-1472
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Tidskriftsartikel (refereegranskat)abstract
- Magnetic resonance imaging (MRI) is the first-line imaging modality for local staging of rectal cancer. The radiology report should deliver all relevant available imaging information to guide treatment. Purpose To explore and describe if there was a gap between the contents in MRI reports for primary staging of rectal cancer in Sweden in 2010 compared to evidence-based practice. Material and Methods A total of 243 primary MRI staging reports from 2010, collected from 10 hospitals in four healthcare regions in Sweden, were analyzed using content analysis with a deductive thematic coding scheme based on evidence-based practice. Focus was on: (i) most frequently reported findings; (ii) correlation to key prognostic findings; and (iii) identifying if any findings being reported were beyond the information defined in evidence-based practice. Results Most frequently reported findings were spread through the bowel wall or not, local lymph node description, tumor length, and distance of tumor from anal verge. These items accounted for 35% of the reporting content. Of all reported content, 86% correlated with the evidence-based practice. However, these included more information than was generally found in the reports. When adjusting for omitted information, 48% of the reported content were accounted for. Of the reported content, 20% correlated to key pathological prognostic findings. Six types of findings were reported beyond the evidence-based practice, representing 14% of the total reporting content. Conclusion There was a gap between everyday practice and evidence-based practice in 2010. This indicates a need for national harmonization and implementation of standardized structured reporting templates.
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| 4. |
- Kördel, Mikael, et al.
(författare)
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Quantitative conversion of biomass in giant DNA virus infection
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Bioconversion of organic materials is the foundation of many applications in chemical engineering, microbiology and biochemistry. Herein, we introduce a new methodology to quantitatively determine conversion of biomass in viral infections while simultaneously imaging morphological changes of the host cell. As proof of concept, the viral replication of an unidentified giant DNA virus and the cellular response of an amoebal host are studied using soft X-ray microscopy, titration dilution measurements and thermal gravimetric analysis. We find that virions produced inside the cell are visible from 18 h post infection and their numbers increase gradually to a burst size of 280-660 virions. Due to the large size of the virion and its strong X-ray absorption contrast, we estimate that the burst size corresponds to a conversion of 6-12% of carbonaceous biomass from amoebal host to virus. The occurrence of virion production correlates with the appearance of a possible viral factory and morphological changes in the phagosomes and contractile vacuole complex of the amoeba, whereas the nucleus and nucleolus appear unaffected throughout most of the replication cycle.
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| 5. |
- Sobolev, Egor, et al.
(författare)
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Megahertz single-particle imaging at the European XFEL
- 2020
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Ingår i: Communications Physics. - : Springer Science and Business Media LLC. - 2399-3650. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is expected to provide 27,000 pulses per second, over two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The results obtained pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.
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