| 1. |
- Nelson, G., et al.
(författare)
-
QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
- 2021
-
Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 284:1, s. 56-73
-
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.
|
|
| 2. |
- Xylouris, Georgios, et al.
(författare)
-
Experimentation and 5G KPI measurements in the 5GENESIS platforms
- 2021
-
Ingår i: 5G-MeMU '21. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450386364 ; , s. 1-7
-
Konferensbidrag (refereegranskat)abstract
- The adoption of 5G has recently picked up pace and across the globe commercial deployments are more and more numerous. In addition to better performance, 5G brings, among others, management and operation flexibility, thus allowing industry verticals to exploit features of the telecommunication networks that go far beyond the new mobile access capabilities. As with any new technology, the integration, testing and validation of new vertical applications pose great challenges at both management and operational levels. In this context, there is an evident need for 5G infrastructure facilities that offer testing and validation capabilities through a flexible experimentation framework. This paper presents the 5GENESIS EU-funded research project Experimentation Facility and the results of the validation campaigns conducted in its five experimentation platforms. The tests and obtained results were facilitated by the 5GENESIS Suite, an open-source framework providing test automation and result analytics.
|
|
| 3. |
- Aumayr, E., et al.
(författare)
-
Service-based Analytics for 5G open experimentation platforms
- 2022
-
Ingår i: Computer Networks. - : Elsevier B.V.. - 1389-1286 .- 1872-7069. ; 205
-
Tidskriftsartikel (refereegranskat)abstract
- A scalable, flexible and reliable Analytics service has become a requirement toward building efficient Fifth Generation (5G) experimental platforms that can support a suite of end-user experiments and verticals. Our paper presents the challenges that come with designing such a service-based Analytics component, and shows how we have used it in the context of open experimental platforms in the 5GENESIS project. Our Analytics service was designed both for enabling the efficient setup and configuration of the underlying platform, and also for ensuring that it provides useful insights into the experimentation Key Performance Indicators (KPIs) toward the end-user. Thus, Analytics proved to be a useful tool across several stages, starting from ensuring correct operation during the initial phases of the network setup and continuing into the normal day-to-day experimentation. Our experiments show how the tool was used in our setup and provide information on how to apply it to different environments. The Analytics component, designed as a set of microservices that serve several goals in the analytics workflow, is also provided as open source, being part of the Open5Genesis suite.
|
|
| 4. |
- Ueda, Kiyoshi, et al.
(författare)
-
Roadmap on photonic, electronic and atomic collision physics : I. Light-matter interaction
- 2019
-
Ingår i: Journal of Physics B. - : IOP PUBLISHING LTD. - 0953-4075 .- 1361-6455. ; 52:17
-
Tidskriftsartikel (refereegranskat)abstract
- We publish three Roadmaps on photonic, electronic and atomic collision physics in order to celebrate the 60th anniversary of the ICPEAC conference. In Roadmap I, we focus on the light-matter interaction. In this area, studies of ultrafast electronic and molecular dynamics have been rapidly growing, with the advent of new light sources such as attosecond lasers and x-ray free electron lasers. In parallel, experiments with established synchrotron radiation sources and femtosecond lasers using cutting-edge detection schemes are revealing new scientific insights that have never been exploited. Relevant theories are also being rapidly developed. Target samples for photon-impact experiments are expanding from atoms and small molecules to complex systems such as biomolecules, fullerene, clusters and solids. This Roadmap aims to look back along the road, explaining the development of these fields, and look forward, collecting contributions from twenty leading groups from the field.
|
|
| 5. |
- Velicky, Philipp, et al.
(författare)
-
Genome amplification and cellular senescence are hallmarks of human placenta development
- 2018
-
Ingår i: PLOS Genetics. - : PUBLIC LIBRARY SCIENCE. - 1553-7390 .- 1553-7404. ; 14:10
-
Tidskriftsartikel (refereegranskat)abstract
- Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) beta-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM.
|
|
