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| 2. |
- Nelson, G., et al.
(författare)
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QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
- 2021
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 284:1, s. 56-73
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Tidskriftsartikel (refereegranskat)abstract
- A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
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- Mbufong, H. N., et al.
(författare)
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Assessing the spatial variability in peak season CO2 exchange characteristics across the Arctic tundra using a light response curve parameterization
- 2014
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4189. ; 11:17, s. 4897-4912
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Tidskriftsartikel (refereegranskat)abstract
- This paper aims to assess the spatial variability in the response of CO2 exchange to irradiance across the Arctic tundra during peak season using light response curve (LRC) parameters. This investigation allows us to better understand the future response of Arctic tundra under climatic change. Peak season data were collected during different years (between 1998 and 2010) using the micrometeorological eddy covariance technique from 12 circumpolar Arctic tundra sites, in the range of 64-74 degrees N. The LRCs were generated for 14 days with peak net ecosystem exchange (NEE) using an NEE-irradiance model. Parameters from LRCs represent site-specific traits and characteristics describing the following: (a) NEE at light saturation (F-csat), (b) dark respiration (Rd), (c) light use efficiency (alpha), (d) NEE when light is at 1000 mu molm(-2) s(-1) (F-c1000), (e) potential photosynthesis at light saturation (P-sat) and (f) the light compensation point (LCP). Parameterization of LRCs was successful in predicting CO2 flux dynamics across the Arctic tundra. We did not find any trends in LRC parameters across the whole Arctic tundra but there were indications for temperature and latitudinal differences within sub-regions like Russia and Greenland. Together, leaf area index (LAI) and July temperature had a high explanatory power of the variance in assimilation parameters (F-csat, F-c1000 and P-sat), thus illustrating the potential for upscaling CO2 exchange for the whole Arctic tundra. Dark respiration was more variable and less correlated to environmental drivers than were assimilation parameters. This indicates the inherent need to include other parameters such as nutrient availability, substrate quantity and quality in flux monitoring activities.
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- Boehm, U., et al.
(författare)
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QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy
- 2021
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; :18, s. 1423-1426
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Tidskriftsartikel (refereegranskat)abstract
- The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for hardware calibration and image acquisition, management and analysis.
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| 6. |
- Lund, Magnus, et al.
(författare)
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Low impact of dry conditions on the CO2 exchange of a Northern-Norwegian blanket bog
- 2015
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Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 10:2
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Tidskriftsartikel (refereegranskat)abstract
- Northern peatlands hold large amounts of organic carbon (C) in their soils and are as such important in a climate change context. Blanket bogs, i.e. nutrient-poor peatlands restricted to maritime climates, may be extra vulnerable to global warming since they require a positive water balance to sustain their moss dominated vegetation and C sink functioning. This study presents a 4.5 year record of land-atmosphere carbon dioxide (CO2) exchange from the Andoya blanket bog in northern Norway. Compared with other peatlands, the Andoya peatland exhibited low flux rates, related to the low productivity of the dominating moss and lichen communities and the maritime settings that attenuated seasonal temperature variations. It was observed that under periods of high vapour pressure deficit, net ecosystem exchange was reduced, which was mainly caused by a decrease in gross primary production. However, no persistent effects of dry conditions on the CO2 exchange dynamics were observed, indicating that under present conditions and within the range of observed meteorological conditions the Andoya blanket bog retained its C uptake function. Continued monitoring of these ecosystem types is essential in order to detect possible effects of a changing climate.
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