| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Aalbers, J., et al.
(författare)
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A next-generation liquid xenon observatory for dark matter and neutrino physics
- 2023
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Ingår i: Journal of Physics G: Nuclear and Particle Physics. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 50:1
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Forskningsöversikt (refereegranskat)abstract
- The nature of dark matter and properties of neutrinos are among the most pressing issues in contemporary particle physics. The dual-phase xenon time-projection chamber is the leading technology to cover the available parameter space for weakly interacting massive particles, while featuring extensive sensitivity to many alternative dark matter candidates. These detectors can also study neutrinos through neutrinoless double-beta decay and through a variety of astrophysical sources. A next-generation xenon-based detector will therefore be a true multi-purpose observatory to significantly advance particle physics, nuclear physics, astrophysics, solar physics, and cosmology. This review article presents the science cases for such a detector.
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| 3. |
- Allanach, Benjamin C., et al.
(författare)
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Simple and statistically sound strategies for analysing physical theories
- 2022
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Ingår i: Reports on progress in physics (Print). - : Institute of Physics Publishing (IOPP). - 0034-4885 .- 1361-6633. ; 85:5
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Forskningsöversikt (refereegranskat)abstract
- Physical theories that depend on many parameters or are tested against data from many different experiments pose unique challenges to statistical inference. Many models in particle physics, astrophysics and cosmology fall into one or both of these categories. These issues are often sidestepped with statistically unsound ad hoc methods, involving intersection of parameter intervals estimated by multiple experiments, and random or grid sampling of model parameters. Whilst these methods are easy to apply, they exhibit pathologies even in low-dimensional parameter spaces, and quickly become problematic to use and interpret in higher dimensions. In this article we give clear guidance for going beyond these procedures, suggesting where possible simple methods for performing statistically sound inference, and recommendations of readily-available software tools and standards that can assist in doing so. Our aim is to provide any physicists lacking comprehensive statistical training with recommendations for reaching correct scientific conclusions, with only a modest increase in analysis burden. Our examples can be reproduced with the code publicly available at Zenodo.
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| 4. |
- Betti, M. G., et al.
(författare)
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A design for an electromagnetic filter for precision energy measurements at the tritium endpoint
- 2019
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Ingår i: Progress in Particle and Nuclear Physics. - : Elsevier BV. - 0146-6410 .- 1873-2224. ; 106, s. 120-131
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Forskningsöversikt (refereegranskat)abstract
- We present a detailed description of the electromagnetic filter for the PTOLEMY project to directly detect the Cosmic Neutrino Background (CNB). Starting with an initial estimate for the orbital magnetic moment, the higher-order drift process of E x B is configured to balance the gradient-B drift motion of the electron in such a way as to guide the trajectory into the standing voltage potential along the mid-plane of the filter. As a function of drift distance along the length of the filter, the filter zooms in with exponentially increasing precision on the transverse velocity component of the electron kinetic energy. This yields a linear dimension for the total filter length that is exceptionally compact compared to previous techniques for electromagnetic filtering. The parallel velocity component of the electron kinetic energy oscillates in an electrostatic harmonic trap as the electron drifts along the length of the filter. An analysis of the phase-space volume conservation validates the expected behavior of the filter from the adiabatic invariance of the orbital magnetic moment and energy conservation following Liouville's theorem for Hamiltonian systems.
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| 5. |
- Conrad, Jan, et al.
(författare)
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Indirect dark matter searches in gamma and cosmic rays
- 2017
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Ingår i: Nature Physics. - 1745-2473 .- 1745-2481. ; 13:3, s. 224-231
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Forskningsöversikt (refereegranskat)abstract
- Dark matter candidates such as weakly interacting massive particles are predicted to annihilate or decay into Standard Model particles, leaving behind distinctive signatures in gamma rays, neutrinos, positrons, antiprotons, or even antinuclei. Indirect dark matter searches, and in particular those based on gamma-ray observations and cosmic-ray measurements, could detect such signatures. Here we review the strengths and limitations of this approach and look into the future of indirect dark matter searches.
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| 6. |
- Conrad, Jan
(författare)
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Statistical issues in astrophysical searches for particle dark matter
- 2015
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Ingår i: Astroparticle physics. - : Elsevier BV. - 0927-6505 .- 1873-2852. ; 62, s. 165-177
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Forskningsöversikt (refereegranskat)abstract
- In this review statistical issues appearing in astrophysical searches for particle dark matter, i.e. indirect detection (dark matter annihilating into standard model particles) or direct detection (dark matter particles scattering in deep underground detectors) are discussed. One particular aspect of these searches is the presence of very large uncertainties in nuisance parameters (astrophysical factors) that are degenerate with parameters of interest (mass and annihilation/decay cross sections for the particles). The likelihood approach has become the most powerful tool, offering at least one well motivated method for incorporation of nuisance parameters and increasing the sensitivity of experiments by allowing a combination of targets superior to the more traditional data stacking. Other statistical challenges appearing in astrophysical searches are to large extent similar to any new physics search, for example at colliders, a prime example being the calculation of trial factors. Frequentist methods prevail for hypothesis testing and interval estimation, Bayesian methods are used for assessment of nuisance parameters and parameter estimation in complex parameter spaces. The basic statistical concepts will be exposed, illustrated with concrete examples from experimental searches and caveats will be pointed out.
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| 7. |
- Conrad, Jan, et al.
(författare)
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Wimp searches with gamma rays in the Fermi era : Challenges, methods and results
- 2015
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Ingår i: Journal of Experimental and Theoretical Physics. - 1063-7761 .- 1090-6509. ; 121:6, s. 1104-1135
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Forskningsöversikt (refereegranskat)abstract
- The launch of the gamma-ray telescope Fermi Large Area Telescope (Fermi-LAT) started a pivotal period in indirect detection of dark matter. By outperforming expectations, for the first time a robust and stringent test of the paradigm of weakly interacting massive particles (WIMPs) is within reach. In this paper, we discuss astrophysical targets for WIMP detection and the challenges they present, review the analysis tools which have been employed to tackle these challenges, and summarize the status of constraints on and the claimed detections in the WIMP parameter space. Methods and results will be discussed in comparison to Imaging Air Cherenkov Telescopes. We also provide an outlook on short term and longer term developments.
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| 8. |
- Damoiseaux, Jan, et al.
(författare)
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Autoantibodies and SARS-CoV2 infection : The spectrum from association to clinical implication. Report of the 15th Dresden Symposium on Autoantibodies
- 2022
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Ingår i: Autoimmunity Reviews. - : Elsevier. - 1568-9972 .- 1873-0183. ; 21:3
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Forskningsöversikt (refereegranskat)abstract
- The relation between infections and autoimmune diseases has been extensively investigated. Multiple studies suggest a causal relation between these two entities with molecular mimicry, hyperstimulation and dysregulation of the immune system as plausible mechanisms. The recent pandemic with a new virus, i.e., SARS-CoV-2, has resulted in numerous studies addressing the potential of this virus to induce autoimmunity and, eventually, autoimmune disease. In addition, it has also revealed that pre-existing auto-immunity (auto-Abs neutralizing type I IFNs) could cause life-threatening disease. Therefore, the topic of the 15th Dresden Symposium on Autoantibodies was focused on autoimmunity in the SARS-CoV-2 era. This report is a collection and distillation of the topics presented at this meeting.
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