| 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. |
- Adamczewski-Musch, J., et al.
(författare)
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Production and electromagnetic decay of hyperons : a feasibility study with HADES as a phase-0 experiment at FAIR
- 2021
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Ingår i: European Physical Journal A. - : Springer Nature. - 1434-6001 .- 1434-601X. ; 57:4
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Tidskriftsartikel (refereegranskat)abstract
- A feasibility study has been performed in order to investigate the performance of the HADES detector to measure the electromagnetic decays of the hyperon resonances Sigma(1385)(0), Lambda(1405) and Lambda(1520) as well as the production of double strange baryon systems Xi(-) and Lambda Lambda in p + p reactions at a beam kinetic energy of 4.5GeV. The existing HADES detector will be upgraded by a new Forward Detector, which extends the detector acceptance into a range of polar angles that plays a crucial role for these investigations. The analysis of each channel is preceded by a consideration of the production cross-sections. Afterwards the expected signal count rates using a target consisting of either liquid hydrogen or polyethylene are summarized.
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| 3. |
- Gallagher, A. J., et al.
(författare)
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Observational constraints on the origin of the elements II. 3D non-LTE formation of BaII lines in the solar atmosphere
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 634
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Tidskriftsartikel (refereegranskat)abstract
- Context. The pursuit of more realistic spectroscopic modelling and consistent abundances has led us to begin a new series of papers designed to improve current solar and stellar abundances of various atomic species. To achieve this, we have begun updating the three-dimensional (3D) non-local thermodynamic equilibrium (non-LTE) radiative transfer code, MULTI3D, and the equivalent one-dimensional (1D) non-LTE radiative transfer code, MULTI 2.3.Aims. We examine our improvements to these codes by redetermining the solar barium abundance. Barium was chosen for this test as it is an important diagnostic element of the s-process in the context of galactic chemical evolution. New BaII + H collisional data for excitation and charge exchange reactions computed from first principles had recently become available and were included in the model atom. The atom also includes the effects of isotopic line shifts and hyperfine splitting.Methods. A grid of 1D LTE barium lines were constructed with MULTI 2.3 and fit to the four BaII lines available to us in the optical region of the solar spectrum. Abundance corrections were then determined in 1D non-LTE, 3D LTE, and 3D non-LTE. A new 3D non-LTE solar barium abundance was computed from these corrections.Results. We present for the first time the full 3D non-LTE barium abundance of A(Ba) = 2.27 +/- 0.02 +/- 0.01, which was derived from four individual fully consistent barium lines. Errors here represent the systematic and random errors, respectively.
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| 4. |
- Kurbanov, R.N., et al.
(författare)
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A detailed luminescence chronology of the Lower Volga loess-palaeosol sequence at Leninsk
- 2022
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Ingår i: Quaternary Geochronology. - : Elsevier. - 1871-1014 .- 1878-0350. ; 73
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Tidskriftsartikel (refereegranskat)abstract
- We present a detailed luminescence chronology of the loess-palaeosol sequences in the Lower Volga region of Russia at the Leninsk site – an important palaeogeographic archive describing the climate and environmental conditions of regressive stages of the Caspian Sea. The chronology of these sediments has received very little attention compared to the under- and overlying marine deposits. The degree of bleaching was addressed by making use of the differential resetting rates of quartz and feldspar. Our results show that the quartz OSL and feldspar pIRIR50,290 signals were sufficiently bleached before deposition and uncertainties in bleaching have a negligible impact on the reliability of the luminescence ages. The combined quartz OSL and K-feldspar pIRIR50,290 chronology constrains the main stages of the Northern Caspian Lowland evolution during the Late Quaternary. During early MIS 5 (130–120 ka), the northern part of the Lower Volga was covered by a shallow brackish water estuary of the warm Late Khazarian Caspian Sea transgression. After ∼122 ka, the Volga incised the Northern Caspian Lowland surface following sea-level decrease and the start of subaerial conditions at Leninsk. Loess accumulation rate increased towards the end of MIS 5 and two palaeosols of presumably MIS 5с and MIS 5a age formed, exhibiting features evidencing a dry, cold climate, influenced by long seasonal flooding by the Volga River. Cryogenesis affecting the MIS 5a soil is a regional phenomenon and is dated to between ∼70 and 90 ka. The overlying thick Atelian loess unit formed during the cold periods of MIS 4 and MIS 3. Clear erosional features at the top of the Atelian loess are constrained by luminescence to ∼35 to ∼24 ka, allowing reconstruction of erosion of 150–200 cm of loess.
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| 5. |
- Storm, N., et al.
(författare)
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3D NLTE modelling of Y and Eu : Centre-to-limb variation and solar abundances
- 2024
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 683
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Tidskriftsartikel (refereegranskat)abstract
- Context: Abundances of s- and r-process elements in Sun-like stars constrain nucleosynthesis in extreme astrophysical events, such as compact binary mergers and explosions of highly magnetised rapidly rotating massive stars.Aims: We measure solar abundances of yttrium (Y) and europium (Eu) using 3D non-local thermal equilibrium (NLTE) models. We use the model to determine the abundance of Y, and also explore the model's ability to reproduce the solar centre-to-limb variation of its lines. In addition, we determine the Eu abundance using solar disc-centre and integrated flux spectra.Methods: We developed an NLTE model of Eu and updated our model of Y with collisional data from detailed quantum-mechanical calculations. We used the IAG spatially resolved high-resolution solar spectra to derive the solar abundances of Y across the solar disc and of Eu for integrated flux and at disc centre using a set of carefully selected lines and a 3D radiation-hydrodynamics model of the solar atmosphere.Results: We find 3D NLTE solar abundances of A(Y)(3D NLTE) = 2.30 ± 0.03stat ± 0.07syst dex based on observations at all angles and A(Eu) = 0.57 ± 0.01stat ± 0.06syst dex based on the integrated flux and disc-centre intensity. 3D NLTE modelling offers the most consistent abundances across the solar disc, and resolves the problem of severe systematic bias in Y and Eu abundances inherent to 1D LTE, 1D NLTE, and 3D LTE modelling.
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| 6. |
- Tikhonenkov, Denis, V, et al.
(författare)
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On the origin of TSAR : morphology, diversity and phylogeny of Telonemia
- 2022
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Ingår i: Open Biology. - : The Royal Society. - 2046-2441. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- Telonemia is a poorly known major phylum of flagellated eukaryotes with a unique combination of morphological traits. Phylogenomics recently revealed the phylogenetic position of telonemids as sister to SAR, one of the largest groups of eukaryotes, comprising Stramenopiles, Alveolata and Rhizaria. Due to this key evolutionary position, investigations of telonemids are of critical importance for elucidating the origin and diversification of an astounding diversity of eukaryotic forms and life strategies. To date, however, only two species have been morphologically characterized from Telonemia, which do not represent this genetically very diverse group. In this study, we established cultures for six new telonemid strains, including the description of five new species and a new genus. We used these cultures to update the phylogeny of Telonemia and provide a detailed morphological and ultrastructural investigation. Our data elucidate the origin of TSAR from flagellates with complex morphology and reconstruction of the ancestral structure of stramenopiles, alveolates and rhizarians, and their main synapomorphic characters. Since telonemids are a common component of aquatic environments, the features of their feeding, behaviour and ecological preferences observed in clonal cultures and the results of global metabarcoding analysis contribute to a deeper understanding of organization of microbial food webs.
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