| 1. |
- 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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| 2. |
- 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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| 3. |
- Binder, Zev A., et al.
(författare)
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Epidermal Growth Factor Receptor Extracellular Domain Mutations in Glioblastoma Present Opportunities for Clinical Imaging and Therapeutic Development
- 2018
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Ingår i: Cancer Cell. - : Elsevier BV. - 1535-6108 .- 1878-3686. ; 34:1, s. 163-177
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Tidskriftsartikel (refereegranskat)abstract
- We explored the clinical and pathological impact of epidermal growth factor receptor (EGFR) extracellular domain missense mutations. Retrospective assessment of 260 de novo glioblastoma patients revealed a significant reduction in overall survival of patients having tumors with EGFR mutations at alanine 289 (EGFR(A289D/T/V)). Quantitative multi-parametric magnetic resonance imaging analyses indicated increased tumor invasion for EGFR(A289D/T/V) mutants, corroborated in mice bearing intracranial tumors expressing EGFR(A289V) and dependent on ERK-mediated expression of matrix metalloproteinase-1. EGFR(A289V) tumor growth was attenuated with an antibody against a cryptic epitope, based on in silico simulation. The findings of this study indicate a highly invasive phenotype associated with the EGFR(A289V) mutation in glioblastoma, postulating EGFR(A289V) as a molecular marker for responsiveness to therapy with EGFR-targeting antibodies.
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| 4. |
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| 5. |
- Bagley, Mark J. O.
(författare)
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A simulation of entrepreneurial spawning
- 2017
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Ingår i: JASSS. - : University of Surrey. - 1460-7425. ; 20:3
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Tidskriftsartikel (refereegranskat)abstract
- This paper describes how patterns of industrial clustering arise with respect to the size of an initial firm when measured in terms of innovation. Through principles of evolutionary economics, the aim of this paper is to examine the ’birth’ of industrial clusters. We take an endogenous and supply-side approach, where firms in a region spawn from incumbents. Technology is qualitatively described using a code set mapped on a cognitive space. Assuming inheritability of networking skills, we seek to model how the size of an initial firm influences future patterns of cluster formation through a model of technical cognition and a mimicking of creativity. It is found that initial firm size has a lasting impact on clustering patterns through its influence on the level of cognitive distance of the underlying agents. The model replicates the stylised facts of entrepreneurial cluster formation.
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| 6. |
- Bagley, Mark J. O.
(författare)
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Networks in clusters
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- There is a multitude of studies that examine the performance of firms within industrial clusters. The organizational attributes inherited by spinoffs from parent firms is one explanation behind performance premiums. This paper examines the relationship between a spinoff’s network and its geographical location in an industrial cluster. We hypothesize that there is a negative relationship between a spinoff’s network efficiency and its distance from the cluster’s centroid. Although recent literature infers that the transmission of knowledge in industrial clusters is accomplished via passive network ties, this has not been directly measured. This paper aims to fill that research gap. We find that, after controlling for firm size, parent size and age, there is indeed a statistically significant and negative relationship between network efficiency and geographic distance to a cluster’ score.
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| 7. |
- Glover, A. G., et al.
(författare)
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A live video observatory reveals temporal processes at a shelf-depth whale-fall
- 2010
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Ingår i: Cahiers De Biologie Marine. - 0007-9723. ; 51:4, s. 375-381
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Tidskriftsartikel (refereegranskat)abstract
- There have been very few studies of temporal processes at chemosynthetic ecosystems, even at relatively more accessible shallow water sites. Here we report the development and deployment of a simple cabled video observatory at 30 m water depth in Gullmarsfjorden, Sweden. The camera provides a live video feed to the internet of faunal activity in the experiments, which to date have included 5 separate whale-fall deployments. Our data suggest that the time to decomposition of small cetacean carcasses at shelf-depth settings is considerably slower than at deep-sea sites. We have also provided a new methodology for the deployment of low-cost live video observatories at up to 30 m water depth, which can be used both for research and outreach activities.
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