| 1. |
- Alneberg, Johannes, et al.
(författare)
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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
- 2018
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .
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| 2. |
- Larsson, Jim, et al.
(författare)
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A 3-D printed phantom for optical techniques in medicine
- 2017
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Ingår i: CLEO: Applications and Technology, CLEO_AT 2017. - 9781943580279 ; Part F43-CLEO_AT 2017
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Konferensbidrag (refereegranskat)abstract
- Development of optical techniques in medical applications can be difficult due to limited access to realistic phantoms. Here a 3-D printed model based on CT-images of the thorax of an infant is developed and tested.
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| 3. |
- Larsson, Jim, et al.
(författare)
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Development of a 3-dimensional tissue lung phantom of a preterm infant for optical measurements of oxygen—Laser-detector position considerations
- 2018
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Ingår i: Journal of Biophotonics. - : Wiley. - 1864-063X. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- There is a need to further improve the clinical care of our most vulnerable patients—preterm infants. Novel diagnostic and treatment tools facilitate such advances. Here, we evaluate a potential percutaneous optical monitoring tool to assess the oxygen and water vapor content in the lungs of preterm babies. The aim is to prepare for further clinical studies by gaining a detailed understanding of how the measured light intensity and gas absorption signal behave for different possible geometries of light delivery and receiver. Such an experimental evaluation is conducted for the first time utilizing a specially developed 3-dimensional-printed optical phantom based on a geometry model obtained from computer tomography images of the thorax (chest) of a 1700-g premature infant. The measurements yield reliable signals for source–detector distances up to about 50 mm, with stronger gas absorption signals at long separations and positions related to the lower part of the lung, consistent with a larger relative volume of this. The limitations of this study include the omission of scattering tissue within the lungs and that similar optical properties are used for the wavelengths employed for the 2 gases, yielding no indication on the optimal wavelength pair to use.
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| 4. |
- Liao, Peilang, et al.
(författare)
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Computer simulation analysis of source-detector position for percutaneously measured O2-gas signal in a three-dimensional preterm infant lung
- 2018
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Ingår i: Journal of Biophotonics. - : Wiley. - 1864-063X. ; 11:11
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Tidskriftsartikel (refereegranskat)abstract
- Further improvements in the clinical care of our most vulnerable patients-preterm infants-are needed. Novel diagnostic and surveillance tools facilitate such advances. The GASMAS technique has shown potential to become a tool to, noninvasively, monitor gas in the lungs of preterm infants, by placing a laser source and a detector on the chest wall skin. It is believed that this technology will become a valuable clinical diagnostic tool for monitoring the lung function of these patients. Today, the technology is, for this application, in an early stage and further investigations are needed. In the present study, a three-dimensional computer model of the thorax of an infant is constructed, from a set of CT images. Light transport simulations are performed to provide information about the position dependence of the laser- and detector probe on the thorax of the infant. The result of the simulations, based on the study method and the specified model used in this work, indicates that measurement geometries in front and on the side of the lung are favorable in order to obtain a good gas absorption signal.
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