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- Nelson, G., et al.
(author)
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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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In: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 284:1, s. 56-73
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Journal article (peer-reviewed)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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| 3. |
- Baldermann, A., et al.
(author)
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Impact of green clay authigenesis on element sequestration in marine settings
- 2022
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Journal article (peer-reviewed)abstract
- Retrograde clay mineral reactions (reverse weathering), including glauconite formation, are first-order controls on element sequestration in marine sediments. Here, we report substantial element sequestration by glauconite formation in shallow marine settings from the Triassic to the Holocene, averaging 3 +/- 2 mmol.cm(-2).kyr(-1) for K, Mg and Al, 16 +/- 9 mmol.cm(-2).kyr(-1) for Si and 6 +/- 3 mmol.cm(-2).kyr(-1) for Fe, which is similar to 2 orders of magnitude higher than estimates for deep-sea settings. Upscaling of glauconite abundances in shallow-water (0-200 m) environments predicts a present-day global uptake of similar to <= 0.1 Tmol.yr(-1) of K, Mg and Al, and similar to 0.1-0.4 Tmol.yr(-1) of Fe and Si, which is similar to half of the estimated Mesozoic elemental flux. Clay mineral authigenesis had a large impact on the global marine element cycles throughout Earth's history, in particular during 'greenhouse' periods with sea level highstand, and is key for better understanding past and present geochemical cycling in marine sediments.
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- Dietzel, C., et al.
(author)
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SDN-enabled traffic engineering and advanced blackholing at IXPs
- 2017
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In: SOSR 2017 - Proceedings of the 2017 Symposium on SDN Research. - New York, NY, USA : ACM. ; , s. 181-182
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Conference paper (peer-reviewed)abstract
- While the clean slate approach proposed by Software Defined Networking (SDN) promises radical changes in the stagnant state of network management, SDN innovation has not gone beyond the intra-domain level. For the inter-domain ecosystem to benefit from the advantages of SDN, Internet Exchange Points (IXPs) are the ideal place: a central interconnection hub through which a large share of the Internet can be affected. In this demo, we showcase the ENDEAVOUR platform: a new software defined exchange approach readily deployable in commercial IXPs. We demonstrate here our implementations of traffic engineering and Distributed Denial of Service mitigation, as well as how member networks cash in on the advanced SDN-features of ENDEAVOUR, typically not available in legacy networks.
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| 8. |
- Runkler, N, et al.
(author)
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Glycoprotein targeting signals influence the distribution of measles virus envelope proteins and virus spread in lymphocytes
- 2008
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In: The Journal of general virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 89:Pt 3, s. 687-696
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Journal article (peer-reviewed)abstract
- We previously demonstrated the presence of tyrosine-dependent motifs for specific sorting of two measles virus (MV) glycoproteins, H and F, to the basolateral surface in polarized epithelial cells. Targeted expression of the glycoproteins was found to be required for virus spread in epithelia via cell-to-cell fusionin vitroandin vivo. In the present study, recombinant MVs (rMVs) with substitutions of the critical tyrosines in the H and F cytoplasmic domains were used to determine whether the sorting signals also play a crucial role for MV replication and spread within lymphocytes, the main target cells of acute MV infection. Immunolocalization revealed that only standard glycoproteins are targeted specifically to the uropod of polarized lymphocytes and cluster on the surface of non-polarized lymphocytes. H and F proteins with tyrosine mutations did not accumulate in uropods, but were distributed homogeneously on the surface and did not colocalize markedly with the matrix (M) protein. Due to the defective interaction with the M protein, all mutant rMVs showed an enhanced fusion capacity, but only rMVs harbouring two mutated glycoproteins showed a marked decrease in virus release from infected lymphocytes. These results demonstrate clearly that the tyrosine-based targeting motifs in the MV glycoproteins are not only important in polarized epithelial cells, but are also active in lymphocytes, thus playing an important role in virus propagation in different key target cells during acute MV infection.
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