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- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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- Battistoni, G, et al.
(author)
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FLUKA Monte Carlo calculations for hadrontherapy application
- 2013
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In: CERN-Proceedings-2012-002. ; , s. 461-467
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Conference paper (peer-reviewed)abstract
- Monte Carlo (MC) codes are increasingly spreading in the hadrontherapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code for application to hadrontherapy demands accurate and reliable physical models for the description of the transport and the interaction of all components of the expected radiation field (ions, hadrons, electrons, positrons and photons). This contribution will address the specific case of the general-purpose particle and interaction code FLUKA. In this work, an application of FLUKA will be presented, i.e. establishing CT (computed tomography)-based calculations of physical and RBE (relative biological effectiveness)-weighted dose distributions in scanned carbon ion beam therapy.
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- Ballarini, F., et al.
(author)
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The physics of the FLUKA code : Recent developments
- 2007
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In: Advances in Space Research. - Elsevier : Elsevier BV. - 0273-1177 .- 1879-1948. ; 40:9, s. 1339-1349
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Journal article (peer-reviewed)abstract
- FLUKA is a Monte-Carlo code able to simulate interaction and transport of hadrons, heavy ions and electromagnetic particles from few keV (or thermal neutron) to cosmic ray energies in whichever material. The highest priority in the design and development of the code has always been the implementation and improvement of sound and modern physical models. A summary of the FLUKA physical models is given, while recent developments are described in detail: among the others, extensions of the intermediate energy hadronic interaction generator, refinements in photon cross sections and interaction models, analytical on-line evolution of radio-activation and remnant dose. In particular, new developments in the nucleus-nucleus interaction models are discussed. Comparisons with experimental data and examples of applications of relevance for space radiation are also provided.
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- Battistoni, G., et al.
(author)
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The FLUKA code and its use in hadron therapy
- 2008
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In: Nuovo Cimento della Societa Italiana di Fisica C. - Italian Physical Society. - 1124-1896. ; 31:1, s. 69-75
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Journal article (peer-reviewed)abstract
- FLUKA is a multipurpose Monte Carto code describing transport and interaction with matter of a, large variety of particles over a wide energy range ill complex geometries. FLUKA is successfully applied ill several fields, including, but not only particle physics, cosmic-ray physics, dosimetry, radioprotection, hadron therapy. space radiation, accelerator design and neutronics. Here we briefly review recent model developments and provide examples of applications to hadron therapy, including calculation of physical and biological dose for comparison with analytical treatment planning engines as well as beta(+)-activation for therapy monitoring by means of positron emission tomography.
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